Microsoft has a site which claims to help customers compare Windows Server editions with Linux. I stumbled across it while reading David M. Williams blog, and he pointed out a case study on the site involving Uppsala. Since I've lived in Uppsala for many years, I couldn't resist reading on. It turns out that there was no comparison at all. Uppsala hired a Microsoft Gold Certified partner to see if they could increase the security of their windows networks and the conclusion was that Windows Server 2008 is a better product than Windows Server 2003. No mention of Linux at all (except an off-hand remark by a server technician).
It's good to see that Microsoft still knows how to do real FUD.