I tend to prefer Debian builds as well. As mentioned, Aptitude is very nice, though yum works just as well for most stuff EQEmu related. I have build many servers on both Debian and Fedora, but I find the selinux on Fedora can be a bit of a pain sometimes (though that is probably mostly due to my ignorance with selinux).
The setup for either are very similar (mostly just change apt-get to yum or visa versa in guides) and performance seems about the same as well.
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