I've got a TJ that I've put about 40 or 50k in to over the years, it's more of a buggy/rock crawler than a Jeep. Only thing left original is the motor and the front half of the frame! Been through a hard (through the air) multiple end-over-end roll on the rocks and it is still chugging.
I'd look for a 2000 up TJ (get the 4.0 6cyl, it will last forever if you change the oil and is a MUCH stronger motor than the 4cyl). At 2000 they dumped the distributor in favor of coil ignition which is nice. The 2000+ 4.0s are also a bit quieter and produce a bit more power.
Check the inside of the frames for rust - there are holes you can fit a couple of fingers in. If it was up north, the frame could be fucked. Check under the doors and in front of the rear tires for scaling rust on the inside of the frame.
If you are going to take it off road in stock form, look for one with a Dana 44 rear axle. It's a lot more stout than the Dana 35. Probably won't matter with stock tires, but if you ever decide to go a bit bigger, the strength of the 44 rear end is much superior and you'll have a bigger ring and pinion (both of which can easily fail on a Dana 35 with bigger than stock tires).
You can tell it is a Dana 44 if the fill plug is metal. The D35 has a rubber fill plug.
Most of the off road guys like auto trannies, you end up with more effective gearing at low RPMs due to torque converter slip. If you think you'll get into the off road side of things, go auto. They are pretty cheap to rebuild. 97-02 had an all mechanical 3 speed auto which was pretty reliable. In 2003 they replaced it with a 4 speed (4th gear is an overdrive).
Look for one with lower gearing (higher numerical #). Chrysler can tell you the gearing from the VIN # if you give them a call. Look for one with 3.73 or 4.10 gears - the higher the # the more power you'll "feel" and the better it'll perform off road.
I always thought the AC was fine with the 6 cyl (I know 4 cyls have shittier AC). I turned my AC compressor into on board air (can run air tools off it or air up my tires) though. But it was fine in Florida summers.
My jeep is a trailer queen now, I really miss driving it around. I want to get a CJ5 and swap in an LS1 or something with just a mild lift as a street Jeep.