What is highest ranking Web site (according to Alexa's
traffic rankings) that is not owned by Microsoft and
yet runs on Microsoft operating systems?

Hi again, bugbear...

That would be eBay, using Windows 2000 and Microsoft-IIS/5.0
as of  2-Mar-2005, and they actually rank higher than Microsoft
which is 6th on Alexa's list, while eBay is 5th.

These are followed by Go.com in 12th place, Myspace.com in 14th
place, Xanga.com in 15th place, Ebay UK in 18th place, and 
DoubleClick.com in 19th place.

It took me forever, digging through my bookmarks, before I was
able to find the site I've seen which digs out information on
the OS and servers for any site you plug in:
http://news.netcraft.com/


Here's a list of the top 20:

1. Yahoo! 
www.yahoo.com
FreeBSD       unknown
 
2. Microsoft Network (MSN) 
www.msn.com 
Windows Server 2003       Microsoft-IIS/6.0

3. Google 
www.google.com 
Linux       GWS/2.1

4. Passport.net 
www.passport.net 
Windows Server 2003       Microsoft-IIS/6.0

5. EBay 
www.ebay.com 
Windows 2000       Microsoft-IIS/5.0

6. Microsoft Corporation 
www.microsoft.com 
Windows Server 2003       Microsoft-IIS/6.0
 
7. Amazon.com 
www.amazon.com 
Linux
Stronghold/2.4.2 Apache/1.3.6 C2NetEU/2412 Unix mod_fastcgi/2.2.12

8. Fastclick 
www.fastclick.com 
Linux       Apache

9. Google UK 
www.google.co.uk 
Linux       GWS/2.1

10. AOL 
www.aol.com 
unknown       AOLserver/3.4.2

11. BBC Online 
www.bbc.co.uk 
Solaris 9       Apache/2.0.51 Unix

12. Go 
www.go.com 
Windows 2000       Microsoft-IIS/5.0

13. CNN - Cable News Network 
www.cnn.com 
Linux       Apache

14. Myspace.com 
www.myspace.com 
Windows 2000       Microsoft-IIS/5.0

15. Xanga 
www.xanga.com 
Windows Server 2003       Microsoft-IIS/6.0

16. Googlesyndication.com 
www.googlesyndication.com 
Linux       GWS/2.1

17. Blogger.com 
www.blogger.com 
Linux       Apache

18. EBay UK 
www.ebay.co.uk 
Windows 2000       Microsoft-IIS/5.0

19.  Double Click 
www.doubleclick.com 
Windows 2000       Microsoft-IIS/5.0

20.  Casale Media 
www.casalemedia.com 
Linux	Apache


You might also be interested in this Webserver Survey
updated in July 2005 by Netcraft, which has a graph of
'Market Share for Top Servers Across All Domains August
 1995 - July 2005' as well as previous months:
http://news.netcraft.com/archives/web_server_survey.html


Please do not rate this answer until you are satisfied that  
the answer cannot be improved upon by way of a dialog  
established through the "Request for Clarification" process. 
 
sublime1-ga

thanks