My wife and I bought her Wrangler new back in '98. It's a 4.0/auto Sport. At the time we had a rule that at least one daily driver had to be an auto in case one of us messed up a knee. My truck was a stick, so Jeep is an auto.
The auto is a descendant of the old Mopar 904 automatic. Nothing wrong with that transmission short of the lack of overdrive. But with 30-31" tires and 3.07 stock gearing that's not really an issue.
As everybody else has said look for rust. Her passenger front fender is starting to blister. I'll need to do something with it in the next couple years.
Another universal Jeep rule is all Jeeps leak. The seal on the side glass of the heard top has shrunk and in a heavy driving rain it leaks. Doesn't appear to be any replacement gasket for it, but I haven't looked that hard.
When hers needed some work a couple years ago we ordered a bunch of TJ Rubicon parts from the dealer. Got the Rubi springs (about 1" taller than the stock '98 springs), wheels (16" and a little wider/less back space vs the original 15"), later mirrors (glass adjusts in the housing vs. moving the whole housing) & fender flares (a little wider than the faded originals).
When we went to the 16" wheels we needed to get some new tires. She's always been happy with the Mickey Thompson AT's, so we went with them. Went with a E-load rated tire. Yea way overkill for a Wrangler, but the size was right and options were limited in non-mudders. The stiffer carcass of the E rated tires really improved the handling without giving up any ride comfort (for a Wrangler).
The 4.0's will occasionally kill a crank position sensor. They just die, no warning. Not too hard to replace. Just buy a good replacement one. The cheap one lasted under a year. Cheap insurance, keep one in the glove box along with a 10MM socket and ratchet. Do that and you'll probably never need it.
Back when it was still under warranty it needed a steering box and an exhaust manifold. This was with the extended 100K warranty. The seal in the steering box gave out. Swapping steering boxes out is pretty straight forward, and there are some good replacement ones out if the original needs more than a seal.
The exhaust manifold is a welded tubular design. They eventually crack. The replacement probably has 70K miles or more on it and under the right conditions it makes a little noise. I'll be looking into a header and exhaust kit for it when the time comes.
The starter is starting to complain now. I have a good reman sitting on the shelf waiting for the shop lift to be available to swap it out.
My wife has said several times that she lovers her Jeep and doesn't know what she would do if it died. I pointed out that we will just rebuild it, it's a Jeep. That's what you do.