I haven't used one, as I like to take the top off... often. ;) That's a bit harder with the 2 door Unlimited, because it has an extra "bar" in the top. Most of the overhead racks don't work as well with the Unlimited. But, I do know a few people who have added kayak racks, there are a number of options, especially if you have a shorter Jeep (YJ/TJ/JK)...
The KargoMaster Congo rack is probably the easiest, although you'd have to add crossmembers and the actual kayak "baskets" from Thule or Yakima or smthng... http://www.quadratec.com/products/12138_000.htm
Garvin is pretty heavy duty and probably overkill if all you need it for is kayaks... http://www.quadratec.com/products/12041_002_07.htm
Lange is the cheap way to go, but I wouldn't trust it on the spare tire... I've seen what 33" tires can do to the tailgate... I expect a couple kayaks on the stock tire would do about the same. http://www.quadratec.com/products/12031_00_07.htm
Hope that helps... You didn't mention what model Jeep or if you have a hard top. Having the hard top opens up some cheaper options, as you generally don't need to get an entire frame mounted first.