Many Microsoft servers are powered by Linux (searchdns.netcraft.com)

Talking about "dogfooding" http://en.wikipedia.org/wiki/Eating_your_own_dog_food

The "Linux" servers are Akamai's.

AFAIK, the servers itself are all-microsoft, most brobably netcraft.com is confused by load-balancers (akamai or something similar)

This has been going on since windows NT launched (as in, that's when people first found out). They just outsource a lot of their website load to external hosts who run Linux.

Akamai isn't Msft they just have subdomains pointed to it