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.