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I have used both Windows 2k3 and 2k8 and Linux Ubuntu Server and CentOS. So far my best experience has been on CentOS.
The problems with Windows rose with all the service/process issues, and the fact that I was using way to much CPU and RAM for my OS. Switching to Linux provided me much higher quality and quantity for my servers. I am also still learning Linux Command line, and enjoy it a lot more. (Especially Yum commands!)
97% of all major mods work on Linux and Windows, so I see no big issue with that.
I'm not Biased at all, being a Windows user all my life. But Linux is the best for servers not only for performance, but for security.
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If I had to pick a linux OS Id pick CentOS as well, and tweak it to run 1000fps and what not.
Looking for a game server? Visit
fullfrag.com and pick one up as low as $2.50 / mo!
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Linux is also easy to recompile, where it is virtually impossible on Windows.