I realize I'm late to the party but I agree with all the above. When I upgraded to 31" I soon realized the tire wouldn't fit in the stock, upright location anymore. (picture me trying to angle in in there a few times - almost ripping my headliner. Duh!)
If you lay it across your floor it takes up most of your usable cargo space, which I need weekly to haul a tall garbag can of recyclables (my justification to the wife for keep this XJ around). I got an awesome deal on my safari roofrack on Craig's List so it was a no brainer for my to throw my spare up there. I fabbed a bolt down system by drilling some holes and using some HD metal plates and the OEM bolt and spinner nut and then put a protective cover over it to keep out rust and dirt.
The worst part about it being up there is that the center of gravity of my XJ is raised and it could use more (some) weight being mounted to the rear and as low as possible. So I plan to mount my Hi-Lift jack to the cargo floor area rather than the roof rack cause it is really heavy. It is also to much of a pain in the ars for me to check the air pressure in the spare because I had to mount it with the air stem down - so I would have to unbolt it just to get to the stem. I also cannot fit in many parking garages because of the added height. So ... Its waay better to spend the money, if you have it, on a rear mount setup.