Greg Nelson, 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.

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

The pair–pictured above, with Morrissey on left, Nelson on right–will have their hands full in what will ultimately be a two-year effort.

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

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

Yahoo confirmed the break to BoomTown.

In recent days, some 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.

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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.

Other good news: A pair of bullish analyst reports yesterday.

But, a spate of executive departures, with chances of more to come, are worrisome.

As is the excessive yodeling Yahoo is once again encouraging.

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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 was later made into a movie)–had been VP of platform engineering at Yahoo 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 also escape the turmoil at Yahoo.

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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 one of Yahoo’s flagship properties 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 –will remain in the U.S., largely located at its Santa Monica, Calif., office.

Yahoo confirmed the change to BoomTown yesterday.

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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 was also no longer on its About page.

According to several sources I spoke to, Henderson was actually not laid off at Yahoo, 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.

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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 the deal can be sealed–I think that Microsoft CEO Steve Ballmer’s top choice is former Yahoo tech star Qi Lu.

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 posted 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.

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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 includes Yahoo CEO Jerry Yang, who is in New York this week–where AOL parent, Time Warner, is located–to meet once again with its CEO, Jeff Bewkes, to see if they can actually complete the merger.

Now, all this frantic activity does not mean a deal will necessarily be struck.

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

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As BoomTown reported earlier today, well-regarded top Yahoo techie Qi Lu will be leaving, 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, said the departure was a “blow” that will be devastating to the engineering organization at Yahoo.

It also looks as though the departure of Search SVP Vish Makhijani will also be announced today or tomorrow, although the fate of Brad Garlinghouse, the SVP who heads communications and communities, is still undetermined but precarious.

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