I have maintained Java apps running on FreeBSD servers, it was a nightmare. And don't even dream of doing that in OpenBSD (which IMHO is the sanest BSD and even nix around).
I've deployed onto primarily Solaris and various flavors of Linux with no problems, but don't have much experience with *BSD... though I've generally assumed it would be a similar experience.
Problems like having to patch and build your own Java runtime because (if you are lucky and there is a working one) because Sun made it illegal to distribute modified Java distributions that had not passed the test-kit, and everyone should know that Sun/Oracle do not give access to the test-kit to anyone that doesn't pay them a ton of $$$.
I've deployed onto primarily Solaris and various flavors of Linux with no problems, but don't have much experience with *BSD... though I've generally assumed it would be a similar experience.