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Others have said it best, go with whatever the folks maintaining the server are most familiar with with. In the end, there isn't a lot of difference performance wise and such, if ran by competent sys-admins.
I prefer Linux, simply because I *know* linux. If anything happens on Linux, there is a good chance I can recovery/fix it. FreeBSD however, I only know the basics.
If ran by competent folks, you will have a good experience with either.
-Phil
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