We just built out our first server with cPanel on FreeBSD. The installation went pretty smooth, but there were some quirks that you'll have to work around. I remember dealing with a lot of startup script problems in the beginning, some issues with enabling qoutas, and a few other little things... with proftpd I think. Unfortunately I didn't take notes.
Anyway, you should have some freebsd administration experience if you're going to use cPanel there. I think Linux cPanel installations are more "plug and play" if you know what I mean.
I don't want to start a holy war, but I prefer FreeBSD over linux, in general, as a server operating system. Though there situations where one or the other OS will excel.