My ZJ feel noticably different (as in BAD) with the tire on the roof. I had my 32"tire and High lift on the factory rack, with the tire resting on the rubber strips of the roof, and it felt weird and top heavy. I put the spare back in the OEM location (just barely... it fit) and I put the high lift across the back of the rear seats, and secured them. It feels much better now, and was well worth the storage space.
I know plenty of people who have their spares on top, and seem to be just fine, but I won't do it anymore.