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FreeBSD is still the best choice in terms of security, although alot of it also depends on what applications you run and how your file systems are setup on either FreeBSD or Linux.
Linux overall is more current with support for hardware but for the most part if you arent on bleeding edge hardware the support for FreeBSD is one-two months off from product launch, especially if you stick to name-brand servers like DELL, etc.
Linux always requires more work to secure it and for the most part alot of installations also depend on how they are actually installed as they are a lot more bulky than FreeBSD, so although it is more compatible and better in a lot of regards, if you havent really researched how to tighten up security you will be quite vulnerable.
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Take Luck!
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