Some interesting stats on Web Site Defacements by OS and Web Server
Linux leads Windows by a wide margin. It's interesting though that the synopsis is not that Windows has improved greatly from a web server security perspective, but rather, that people migrated from Windows to Linux and thus the sites are still attacked.
I got the link from Slashdot. I didn't bother to look at the comments there because I pretty much can already guess what they say. Check for yourself and form your own conclusion.
http://www.zone-h.org/content/view/14928/30/
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