It will be very hard to get into a flamewar with me supporting the Microsoft side of things. That said, none of the links you posted prove anything regarding performance, they do prove something about total cost of ownership, which once you factor everything in leans towards Linux for most installations, however, just looking at the situation for SO seems to me to suggest that they were more comfortable doing the initial development on the stack they were most familiar with and when the license costs started to count against them they used Linux machines to scale out.
Which is a pretty smart decision. Whether an MS stack at this scale is unusual does not say anything at all about whether or not it performs well.
I think we agree for the SE team, given the founders were MS stack familiar, it makes sense.
However, I have to disagree on your assertion the 'Nix's are less performant than the MS stack. The top tier web companies are not running 'Nix because TCO is lower; for most of these companies licensing costs are negligible and if it helped to scale better, it may even save them money going with MS stack... but they don't go with a MS stack...
Sometimes a RHEL license can even cost more than a MS license. Couple that with an Oracle DB back-end, and you easily have a much more costly setup than the MS equivalent. It's not about the money.
These companies are choosing the 'Nix stack because it is performing in an entirely different level than the MS stack. Everything from tiny embedded systems with 64k ram, up to monster systems with TB's of ram.
> "I Contribute to the Windows Kernel. We Are Slower Than Other Operating Systems. Here Is Why."
http://blog.zorinaq.com/?e=74
Which is a pretty smart decision. Whether an MS stack at this scale is unusual does not say anything at all about whether or not it performs well.