Greg Nelson (pictured here), who has had the thankless job of running MSN for Microsoft, has left that position and been given the even more thankless task of running the integration of the complex search and online advertising partnership struck by the software giant and Yahoo.

Microsoft (MSFT) sent out an internal email to staff about the move for the GM of MSN’s Global Media Group, which has already taken place.

MSN U.S. head Scott Moore is now reporting directly to MSN Corporate VP Erik Jorgensen. So will Brett Wayn, who has been working under Nelson on international coordination and who has taken over MSN’s international business on an interim basis.

Nelson’s counterpart at Yahoo (YHOO), according to sources, will be Mark Morrissey (pictured here), who is currently SVP of Products at the Internet giant.

The pair will have their hands full in what will ultimately be a two-year effort, sources estimate, to try to improve their competitive edge against Google (GOOG) in the search arena.

BoomTown’s title for the relationship: A Couple of White Geek Guys Sitting Around Arguing!

The role includes coordinating a massive shift of engineering talent from Yahoo to Microsoft, making sure ad systems are copacetic and most of all, smoothing over what is likely to be a number of bumps in the partnership.

To help make the frustrations less frustrating, there is a $50 million annual payment to Yahoo by Microsoft for three years, for unspecified “transition and implementation costs.”

At least 400 Yahoo employees will be hired by Microsoft, which will also provide funds for retention packages to keep 150 more Yahoos motivated during the transition.

The “Definitive Agreement” between the Silicon Valley company and the Redmond, Wash.-based Microsoft, which had been slated to be signed by Oct. 27, 2009, is about to be completed.

Then, as soon as regulatory approvals are in place, it will be showtime for Nelson and Morrissey.

Longtime Yahoo tech leader Ash Patel is taking some time off until early 2010.

Yahoo (YHOO) confirmed the break to BoomTown.

In recent days, many inside the company had mistakenly thought the 44-year-old EVP for Product Architecture & Strategy was departing the company for good.

Actually, it’s more of a sabbatical for Patel (pictured here).

“Ash will be taking some well-deserved time off to spend time with his family,” said Yahoo in a statement to me. “He will be returning to Yahoo! in early 2010.”

In his latest of many jobs at Yahoo, where he has been employed since 1996, Patel works with its products organization, run by CTO and EVP of Products Ari Balogh, “to drive the development of a comprehensive product strategy, as well as potential strategic deals, helping to evolve and evaluate its audience product and technology strategy.”

It’s one of many leadership positions Patel has had at Yahoo, as the company has reorganized many times over the years, including as EVP of its Audience Products Division, EVP of Platforms and Infrastructure, SVP of Platform Engineering and chief product officer.

He also played a key role as architect of several major Yahoo products, such as MyYahoo!, Yahoo! Finance, Yahoo! Messenger, Yahoo! Chat and many others.

In fact, Patel ended up in a major exec role in a reorg that former Yahoo CEO and co-founder Jerry Yang did in the summer of 2008.

But the appointment of Patel to head the new Global Products group was greeted with some internal dissent, since many were pushing for faster change and new management at the Silicon Valley icon.

Yang was said to have insisted that Patel remain on as planned. He reported directly to President Sue Decker.

Patel stayed on after new CEO Carol Bartz got the top job in January, which was the subject of much interest among longtime Yahoo staff, since he has been one of the few true Yahoo veterans left in a high-ranking role.

In another reorg in late February, this time by Bartz, Patel got his latest title and was placed under Balogh.

Here is a video interview I did with Patel last December about the launch of some open and social networking initiatives at Yahoo (SVP Tapan Bhat, who had once reported to Patel, is also in the video):

In one week, Yahoo will report its third-quarter earnings, after the market closes.

And so far, its stock is showing signs that investors are hoping for better days ahead for the Internet giant.

Shares are up 8.5 percent for the month, almost 13 percent for the last three months and almost 39 percent since the beginning of the year.

While that’s not the rocket ship Google (GOOG) has been on–the search giant’s stock is up 70 percent since January, which includes a big boost recently on expectations of a strong earnings report tomorrow–it’s clear investors are hoping an improvement in the online advertising market will boost Yahoo’s fortunes.

Wall Street is expecting $1.12 billion in net revenue and seven cents in earnings per share from Yahoo (YHOO)–and a better performance than that could boost the stock.

In fact, a pair of bullish analyst reports that came out today predicted just that.

Broadpoint AmTech analyst Benjamin Schachter raised his price target to $21 a share, noting that after the search and online advertising partnership deal closes, Yahoo “should be meaningfully smaller and leaner, but should also be a significantly more profitable company.”

And Benchmark Co. analyst Clayton Moran moved Yahoo from hold to buy, with a price target of $20.

But a string of recent exec departures in Yahoo’s advertising units are making some within the company’s ranks slightly worried.

The departures include Jim Schinella, the company’s SVP for corporate partnerships, in September.

And yesterday, Glam Media announced that it had nabbed Josh Jacobs as SVP of Brand Advertising Products & Marketing. At Yahoo, Jacobs was a key exec in its display ad platform unit.

Many inside the company expect more departures in the ad and engineering arena at Yahoo, pointing out that many big stock packages given to hold onto talent are about to vest.

In addition, once Yahoo’s search and online advertising partnership with Microsoft (MSFT) is approved, as it is likely to be by the end of the year, hundreds of Yahoo engineers will get the choice of moving to Microsoft.

Some will, of course, but some simply do not want to go and many Silicon Valley companies and start-ups BoomTown spoke to report seeing more resumes recently from Yahoo staff.

There is little Microsoft can do to stop possible leakage of tech talent from Yahoo until the deal is approved, since the companies cannot do any integration until it is.

Perhaps worst of all, there seems to be nothing Yahoo can do to stifle its proclivity to yodel, which I begged Yahoo execs to forgo in its recent $100 million “It’s Y!ou” marketing push.

No such luck!

Yesterday, Yahoo launched its online Yodel Studio (no, I am not kidding), where you can record your own yodel in various music genres, like, um, rap.

Yahoo held a kickoff event in New York’s Time Square yesterday–however did I manage to miss it, since I was in Manhattan?–with a passel of celebrity yodelers like Jewel, as well as one in London’s Covent Garden.

Today, there is a yodel event in Mumbai, India. Bollywood yodeling anyone?

Here is a link to the famous Yahoo yodel, by the way, if you are so inclined.

And here is a video of the Times Square event, and also the very memorable Yahoo commercial of Taylor Ware, after she won the Yahoo National Yodel Challenge contest in 2003.

Some things never change (even if they should!).

Eric Boyd (pictured here), a high-profile techie from Yahoo who left the company for a start-up last year, is now headed to Microsoft to work for its digital group, now run by another ex-Yahoo, Qi Lu.

UPDATE: Microsoft confirmed the hiring, although declined to provide further details.

Boyd, who is well-known for his card-counting team exploits while at MIT (which were later made into the movie, “21”) had been VP of platform engineering at Yahoo (YHOO) and worked on a variety of projects there.

With the addition of Boyd, sources said, Microsoft has acquired a huge swath of the top tech talent of Yahoo, many of whom came to the software giant because of Lu and to escape the turmoil at Yahoo.

At a recent tech offsite at Microsoft held by Satya Nadella, SVP of Research and Development at its Online Services division, in fact, one person remarked that a full 10 percent of the techies were former Yahoo execs.

There will be more to come, up to 400 or more, if the search partnership the pair recently struck passes regulatory muster, although Boyd is not part of that deal.

He had worked at Yahoo for a decade, but left last spring to take over as VP of engineering at Mochi Media, a San Francisco-based gaming-related start-up backed $14 million in funding by Shasta Ventures and Accel Partners.

He will be working for Microsoft (MSFT) in Silicon Valley, in its group related to search and advertising, sources said.

In a risky but interesting move that has some at the company nervous and others excited, Yahoo is in the process of moving key development responsibility for its juggernaut Yahoo News unit to Taiwan.

Under the new system, product management, engineering and user interface design for the powerful Yahoo (YHOO) property will become the responsibility of staffers there.

Editorial employees for Yahoo News–which is the No. 1 news site on the Web with 48.4 unique monthly visitors, according to comScore data (SCOR)–will remain in the U.S., largely located at its Santa Monica, Calif., office.

Sources had alerted BoomTown to the change at Yahoo’s flagship content offering this week and many I spoke to about it were deeply worried about further separating key functions in the creation of Yahoo News.

“We are losing more and more of our ability to make quick changes and react to new technologies, which has worked pretty well so far, since we are #1,” said one staffer. “First, we all worked together across a room, then hundreds of miles away and now it is thousands.”

Previously, as was first reported here in February, the distributed and regional method of developing content was shifted to a central global product development organization, with product management, engineering and UI design centered at Yahoo’s Sunnyvale, Calif., HQ under CTO Ari Balogh.

The argument for the shift posits that centralizing the product development of a Yahoo media offering drives efficiencies, saves money, eliminates redundancies and accelerates growth across the world.

Those who do not like the idea think it is wrong to separate the development of a product from the programming because the two are intricately dependent and need to be tweaked delicately.

In addition, they argue, it makes Yahoo media offerings, which have been largely successful, less unique and more dull.

Well, tough tomatoes, because Yahoo confirmed the transition to me when I inquired about it. It was announced internally several weeks ago.

In an interview I did yesterday afternoon with Jeff Kinder, SVP of media products and solutions, who is spearheading the change, he said it was key that Yahoo News streamline how it makes its products in order to be more innovative and responsive on a global basis.

Before the shift to a global system, he pointed out that Yahoo had 26 different news products worldwide, using nine content management systems.

“This is part of building a global media platform,” said Kinder, who leads development of Yahoo’s anchor media properties, as well as its listings and regional products around the world.

Kinder said the staff in Taiwan was selected to take on Yahoo News because it had been creating top-level news products and was passionate about the arena.

Nonetheless, similar functions for other major Yahoo content categories–Sports, Finance and Entertainment–will remain in the United States.

In addition, he noted, with employees in Taiwan taking over these functions at Yahoo News, it would “free up some of the talent” in Silicon Valley to work on other critical content projects.

Kinder dismissed worries about any logjams in the ability of U.S.-based Yahoo News staffers to make changes to offerings, either for consumers or advertising partners, noting there were weekly calls between the teams and plenty of ways to communicate online.

But those worried about the change said the reason for the move was more to cut costs in the content arena, which–like many parts of Yahoo–has undergone layoffs and expense reductions.

Countered Kinder: “We are all driving to the same goal….This is not about cost savings, but about accelerating change and leveraging a global team.”

Yesterday, several Flickr engineers posted news of their layoffs from the Yahoo photo-sharing unit on Twitter, which caused GigaOm’s Om Malik to notice that Flickr architect Cal Henderson (pictured here) was also no longer on its About page.

According to several sources I spoke to, Henderson was actually not laid off at Yahoo (YHOO), but is leaving to start a new company–in the social-gaming arena, I am told–with Flickr co-founder Stewart Butterfield.

He and several other of the original core development team for Flickr transitioned out or have been transitioning out for quite some time, sources said.

Henderson’s Web site, called iamcal.com, still says he is the head of engineering at Flickr.

Butterfield (pictured here), as well as another co-founder, Caterina Fake, left Yahoo last year. Yahoo had paid $35 million to acquire Flickr in 2005.

Fake joined another start-up, called Hunch, last summer as chief product officer. Hunch is an answers site and is now in beta testing.

Yesterday, BoomTown opined that Microsoft was nearing a decision on who would become the head of its digital efforts.

And, according to several sources and some puzzling by me–if an agreement can be reached–I think that Microsoft (MSFT) CEO Steve Ballmer’s top choice is former Yahoo tech star Qi Lu.

While this is by no means a done deal, Lu is just the kind of top tech exec that Ballmer and Microsoft would warm to over a more media-centric choice like former Yahoo COO Dan Rosensweig or former AOL head Jon Miller.

Lu was EVP of engineering for the Search and Advertising Technology Group at Yahoo (YHOO), where he ran all development initiatives for its search and monetization platforms. He was at Yahoo for a decade.

If Ballmer manages to pull off the hire of Lu–on the heels of already grabbing another top Yahoo search exec, Sean Suchter, which I reported on yesterday–the aggressive exec could almost be bypassing a Yahoo search partnership he has long sought by sucking the talent right out of the place instead.

Ballmer is like Edward in “Twilight,” attracting top-notch search execs to Microsoft’s Redmond HQ, as if they were geek versions of Bella.

Lu would be a different choice for the post than many had expected, with a much more technical background than one in online media or advertising sales.

But since all of Microsoft’s future rests on winning in the search and search advertising space and trying to catch up with its archrival Google (GOOG) from way back in the race, Lu is also well suited for the position.

If Lu takes the job, he will be the boss of three strong digital execs at Microsoft: Satya Nadella, the SVP who heads engineering for Microsoft’s search, portal and advertising platform group; Yusuf Mehdi, whose online services portfolio includes marketing, online audience business development and product management for MSN and the search properties; and Brian McAndrews, the SVP for the advertiser and publisher solutions group.

Lu is known as as solid manager, but he is also called a very nice man and unusually humble for a tech star by many, which could be a good influence on Microsoft.

Before Yahoo, Lu was on the staff of the IBM Almaden Research Center, and worked at both Carnegie Mellon University and Fudan University in China (he also got degrees from both places).

And, in the kind of cred Microsoft likes, Lu holds 20 U.S. patents.

He left Yahoo after becoming dissatisfied with all the turmoil there, quitting in June, without another job lined up.

Since he left Yahoo, there have been rumors that he might be headed to Microsoft, but not in such a prominent job.

There has also been speculation that Lu would take a position at Facebook or even return to China for a tech job.

The well-respected Lu certainly has a multitude of choices, but the chance to lead money-laden Microsoft’s digital efforts–as it suits up for battle with Google–is compelling.

BoomTown has been poking around to try to figure out who Ballmer would choose for the digital head, ever since the man who used to be in charge, Kevin Johnson, quit in July, after the software giant’s takeover bid to buy Yahoo failed.

Several people close to the situation say Microsoft’s Ballmer has been keeping the deliberations close to the vest–perhaps because so many of those he has targeted have declined to consider the job.

But this week, many sources both inside and outside the company have told me that Ballmer is close to announcing his choice.

Annoyingly, one source has decided to play a digital version of “The Da Vinci Code” with me, dribbling out clues–more technical than media, very well liked in Silicon Valley, humble–about the candidate, which he wanted me to solve as if I were Robert Langdon and on the hunt for the progeny of Jesus.

Well, my solution is in: Microsoft’s most promising digital Holy Grail is Lu.

On a related note, bizarrely, the day after this column broke the story about Lu’s leaving Yahoo, I caught him by accident in the background of a video I was doing at a Harvard Business School event honoring Facebook’s Mark Zuckerberg.

You can see him at 4:14 minutes in the video, laughing at me, as I bother Greylock Partners VC David Sze and make a bad pun related to former Yahoo exec Jeff Weiner’s departure from Yahoo.

Here’s that video:

Please see this disclosure related to me and Google.

As has been copiously reported here and all over, Yahoo and AOL have been engaged in never-ending talks about a possible deal to merge their flagging Internet businesses.

Now, sources tell me, the circle of executives at both companies interfacing with each other has been widened, for purposes of due diligence.

That chit-chatting includes Yahoo CEO Jerry Yang, who has been in New York several times recently [UPDATE: But not yesterday, in a story I had previously linked to here]–where AOL parent, Time Warner, is located–to meet once with its CEO, Jeff Bewkes, and see if they can actually complete the merger.

Now, all this frantic activity does not mean a deal will necessarily be struck. In fact, in typical Yahoo style, it is going very slowly and that is never a good thing in dealmaking.

But it is this kind of ramped-up blabbery that has many at both companies predicting–hoping, really–that a deal will go through, sooner or later, as soon as Time Warner and Yahoo can agree on a price.

Or, more precisely, a percentage, since Yahoo’s stock price has been falling like a particularly sharp knife of late.

Sources said Yahoo does not want Time Warner (TWX) to have any more than 25 percent of the new company in a trade for AOL’s assets–although that figure would be slightly more if the media giant throws in some of that “Harry Potter”-generated cash into the deal kitty.

Yahoo (YHOO) management, sources said, also think its assets are of significantly better quality than AOL’s, and it still has that powerful–although declining–share in the lucrative search market.

Thus, it does not want to pay the $8 to $10 billion price Time Warner wants, and it should not either. (Here is a good analysis on the price issue by Silicon Alley Insider’s Henry Blodget.)

But Yahoo shares closed yesterday at a troubling $14.58, down 73 cents, or almost five percent.

That means its market valuation also declined by many billion dollars very quickly. It is now at $20.2 billion.

These profound stock drops, said several sources, could spur Yahoo to act before it gets even worse, which is why talks have been more frequent in recent weeks.

While not the best state of mind, panic is always a good motivator, and both companies are surely desperate to turbocharge themselves in the face of tough competition and avoidable management mishaps in recent years.

The hope? That together the pair can do better than they have separately–by combining their advertising, content and communications assets, which are among the largest in the world.

In addition, the “new” Yahoo would be able to make massive cost cuts, including layoffs, under the cover of integration and starting off with a clean slate.

So who would emerge more powerful in a new set-up–AOL or Yahoo?

Here’s a short cheat list:

Content:

AOL and Yahoo have a similar range of content assets, with big sites in all the classic categories, like news, financial, sports and lifestyles. Yahoo’s content head is Scott Moore, while AOL’s is Bill Wilson (both pictured here, left to right).

As I wrote yesterday, I expect that the more dominant Yahoo will rule, slashing and burning most of the AOL-branded properties, keeping only interesting newer brands like sports blog FanHouse, celeb blog TMZ and the Engadget, Tuaw and JoyStiq tech blogs.

And while former Microsoftie Moore is the likely head of this behemoth, don’t count on the very adept Wilson, who is known as a skilled corporate player at AOL, to stick around without a big role in this arena.

Communications:

Again, advantage Yahoo, which has bigger calendaring, email and instant messaging assets, an area once overwhelmingly dominated by AOL. That was then, of course.

Still, AOL’s communications tools are used by a huge audience worldwide and the pair together would be a powerhouse. So much so, in fact, that this might be the one major regulatory hurdle any deal would face.

Advertising:

Again, Yahoo would probably dominate, having just hired well-known former Microsoft exec Joanne Bradford to head up U.S. advertising sales. AOL’s top ad exec is Lynda Clarizio, a former lawyer who is considered dogged but much less experienced than Bradford. (Both are pictured here, right to left.)

And, Yahoo does have its search ad business, however weakening, and a stronger graphical ad business, even if the sector will be most under siege in the current down economy.

Plus, AOL’s Advertising.com, while a major ad network, is more of a business subject to bruising competition and squeezed margins.

Community:

Tapan Bhat (pictured here) now rules community at Yahoo, as well as its homepage, having just inherited it from the departing Brad Garlinghouse.

But AOL has a savvy and voluble exec in Joanna Shields, who came recently via its Bebo social-networking acquisition. While AOL woefully overpaid for Bebo and got played into thinking that other bidders were more interested than they actually were, it was Shields (pictured here) who essentially did that playing.

Sign her up for a top exec role in the combined company pronto!

In all seriousness, there is room for both in the newco, as both AOL and Yahoo seriously bite in the social-networking space. They will surely need a lot more than Bhat and Shields if they want to become true players in Web 2.0’s hottest and probably most important trend.

Engineering:

Yahoo. I do not need to explain this, do I?

Okay: AOL has always been incompetent in the technical arena, since its beginning days, compared with Silicon Valley companies like Yahoo.

All yours, Ash Patel!

Management:

Now, it is here that it gets interesting.

Most feel the push by Yang to do an AOL deal–and make no mistake, it is being pushed by him most of all–is due to increased pressure from his board, as well as major investors, who have had just about enough of his leadership.

“There is no way Jerry stays on as CEO in a newco,” said one source about Yang (pictured here). “He’ll be kicked upstairs as chairman, and I will think [President Sue] Decker will also have to go eventually, since there will be a lot of resistance if she is named CEO.”

But, said other sources, these major management changes will not happen immediately, if at all, as it is too distracting in the wake of a deal and ruins the positive “story” that both companies will surely want to spin.

And spin they will! (Go, Tricia! Go, Jill!)

And while he has a reputation for sharkish political skills, especially compared to Yahoo’s very diplomatic U.S. head, Hilary Schneider, expect AOL President Ron Grant to be an important part of the transition, since he is good–almost too good–at cutting costs.

Most expect his boss, AOL CEO Randy Falco, not to be part of the new company, thereby separating him and Grant, who are nicknamed “Smithers and Burns” at AOL, after “The Simpsons” creepy duo.

Most likely, there will be a search for a top-level CEO to take over the combined company–someone of the stature of New Corp.’s No. 2 Peter Chernin or eBay’s former leader Meg Whitman (except now, she is apparently Sen. John McCain’s pick for Treasury Secretary, if the Republican Presidential candidate were to win the election).

“If this has any chance of working out, the board has to push restart on the leadership,” said one person close to the situation, who notes that this deal is Yang’s last chance to truly impact the future of the company he co-founded and preserve its legacy. “Everyone gets that, even Jerry.”

But I think the idea that Yang would leave if there were to be a merger of Yahoo with AOL is wishful thinking on the part of his critics.

He appears tome to be very committed to seeing his vision of turning around Yahoo through.

And those who have counted him out always seem to be the ones who have been typically wrong, such as Microsoft CEO Steve Ballmer and shareholder activist Carl Icahn.

Because, for all the turmoil at Yahoo, it’s Yang still calling the shots.

As BoomTown reported earlier today, well-regarded top Yahoo techie Qi Lu (pictured here) will be leaving the company, in a move to be announced today or tomorrow by the troubled Internet company.

One Yahoo insider, who characterized Lu as a “rock star” and highly regarded at the company, said the departure was a “blow” that will be devastating to the engineering organization at Yahoo (YHOO).

Our post also alluded to the precarious situation around the top four execs just under Network division head Jeff Weiner, who left last week.

Those execs are: Front Door and Network Services’ Tapan Bhat, Brad Garlinghouse, who heads Yahoo’s communications and communities arenas, Media Group head Scott Moore and Yahoo Search’s Vish Makhijani.

It looks as though the departure of Makhijani (pictured here) will also be announced today or tomorrow.

With Yahoo search just treading water and a deal to outsource some of the search-ad business to Google (GOOG), one has to wonder how Makhijani endured in the center of the storm for this long.

And while there have been reports that Garlinghouse will also leave this week–it was he who started the ball rolling with his infamous “Peanut Butter Manifesto” that called for deep change at Yahoo nearly two years ago–sources tell me he is still sifting through his options, in light of a sweeping reorganization at Yahoo that he is reportedly deeply unhappy about.

That’s why it is more than likely that Garlinghouse (pictured here) will also leave–perhaps by next week–but he has not resigned or told his subordinates of any plans as yet.

But given that power is shifting dramatically to Global Partners Solutions EVP Hilary Schneider in the reorg I wrote about last night, Garlinghouse’s time at Yahoo seems limited.

As I wrote: “Many sources expect that Schneider is likely to amass more power in the new structure–she is close to [Yahoo President Sue] Decker, who must dramatically rejigger Yahoo’s top echelons to better focus the company on its stated objectives of becoming the premier ad network and a consumer ’starting point.’”

More like ending point for a lot of critical Yahoo execs, as repercussions from Yahoo’s botched handling of the Microsoft (MSFT) takeover bid ripple throughout the company.

Memo to Moore and Bhat: If this were a murder mystery, like “Ten Little Indians,” one of you better tread very, very carefully.