I carried my spare on a shell-mounted Yakima roof rack for a few years.
Pros: keeps the tire out of the way, leaves cargo space free, doesn't partially block view out the rear like a tailgate or rear bumper mounted spare.
Cons: adds height, not aerodynamic at all, some wind noise, adds weight at the worst point during off-camber, tippy-crawly situations, can be hard/very hard to get to depending on where you get stuck.
My spare was bolted towards the rear of the rack, so I could get to it by dropping the tailgate and climbing up on it. I could also stand on the rear bumper and unbolt it, but that wasn't nearly as easy. If it was my rig, I'd probably opt for a tailgate/rear bumper spare over a roof mount in most situations (although I do have mine stuffed behind the rear seat at the moment).