<offtopic>I recently discovered puppet and I am just way too excited about what I can do with it.</offtopic>
In theory I think that different stacks (LAMP, Java, and Microsoft were the big contenders at the time) are similar enough in capabilities. There are a million pros and cons to each stack. But I strongly believe that how WELL you know your stack is MUCH more important than WHICH stack you use.
In other words, an experienced Java team will FAR outperform if they can use Java, and an experienced Windows team will FAR outperform if they can use Windows, and the skills of the team are much more significant than the variations between otherwise very very similar platforms. (See also http://www.joelonsoftware.com/items/2006/09/01.html).
So, when we started, Jeff was really good at Microsoft technology, so he was able to produce better code faster using Microsoft technology than if he had to learn Ruby or Python or whatever. And that was BY FAR the dominant decision point for us.
Also, the cost of Windows licenses is virtually insignificant. It's just a non-issue. Not just because of BizSpark (which we took advantage of), but because compiled C# code on Windows servers is so damn efficient you don't need very many servers. Our stack of ten web servers is SHOCKINGLY overprovisioned. They run at insanely low loads now.
Everyone should keep this in mind when they worry about server architecture - SO runs off 12 servers. As long as an app doesn't do anything crazy, it's going to scale very easily throughout the first few years. 1 server should be enough for almost anyone. 1 database, and a few frontend web app servers will take you to millions of views per day.
Unlike user software, most web apps get faster every year, and the stacks tend to get faster (due to better interpreters) not slower (due to silly 3D effects on the desktop).
pg loves to say that people who pay for server software are crazy. That might still be true for Google these days, but not for most people. You don't need many servers, and Windows is no longer slow.
Note : I'm a FSF member and free software fanatic, but I won't pretend that something that obviously works well, doesn't.
And I am genuinely curious as to why you think 12 Windows servers are pain compared to 12 Linux boxes?
The last time I had to work on windows servers SSH wasn't really an option though so we used remote desktop. This was on win2k servers though so things may have changed.
I think the question deserves a better reply than the glib "The same way as you administer any cluster." Is the answer really SSH? Or something else?
There are a few ways of dealing with IIS7:
* Remotely using IIS Manager 
* .NET-style configuration files - think httpd.conf
* Powershell cmdlets
SQL Server has Management Studio in various flavors, SqlCmd.exe or Powershell cmdlets.
The only time I log in to servers is to run installers or when laziness takes hold. These various tools work well enough that Microsoft offers Windows Server Core which only provides CLI access (and Powershell in the most recent version).
The idea that Windows can't be scripted hasn't been true since Perl 5's COM module in the 1990s... Haters always hatin'.
It is a good example of all those stories of not being able to change technology after you become popular. It seems that they are accepting Linux where it fits best at least.
This suggests they're Windows native, but using custom tech to provide non-Windows compatibility.