I wrote this in response to a friend of mine who is looking for a cheap farm/hunting jeep that would replace their side by side. Ultimately, after further discussion he's now searching for a Tracker/Sidekick/Samurai.
You really need to understand that jeep stands for Just Empty Every Pocket. That's a bit tongue and cheek but it's a reference to the fact that they are money pits that are always in need of repair. They're ultimately a Chrysler product and thus have some cost savings flaws that lead to some owners finding them frustratingly difficult to maintain. The worse the condition is that you start with, the more of a nightmare it will be to own. If you can spend a little more on the front end, the cost in time and money to keep it going on the back end will be much much lower.
I would recommend paying somewhere between $7,500-$10,000. That price point will buy you a well cared for 91-02 wrangler. The 5 speed manual transmission, 4.0 h.o 6 cylinder engine will be the most reliable and best performing combination. Do not waste your money on a 4cyl.
The 97-02 (TJ) wranglers will be the most comfortable from a ride standpoint since they are coil spring with a multi-link suspension vs the 91-95 (YJ) jeeps that were leaf sprung. That said, the YJ is a great platform that is slightly less complicated and can likely be found for slightly less money.
The 03-06 wranglers are very similar to the first generation of the TJ. However, they do have some "upgraded" systems that proved to be just as unreliable and ultimately are more expensive to repair. They also demand a higher initial purchase price which in my opinion is unwarranted. If you can find a good deal on one, it is not a deal breaker by any means, but I don't ever recommend anyone seek them out.
Personally, I prefer the 97-99 wranglers. They were in my experience the most reliable years. Not that any of the components very much from later models, but something about those build dates seem to lead to the best owner experience.
There are a lot of jeeps that have been improperly customized. I would do my best to seek out a well equipped jeep, or better yet, one that isn't customized. One of the leading factors to having a bad owner experience is cheap aftermarket parts that lead to snowball effects that compromise longevity. Things like steering component angles that are out of spec from the OEM design. Driveshaft angles that require dropping the skid plate and angling the drivetrain which then oriented the engine mounts, t-case shifter and driveshaft angles in binding positions causing the shifters to be temperamental, u-joints to wear and motor mounts to fail. Those are just examples but there are a laundry list of modifications available for jeeps on the aftermarket that have terrible long term effects.
I can help you navigate these potential problems and guide you toward a good deal. For every 100 jeeps, 90 of them are junk that you don't want. Of the 10 that are worth owning, 7 will be priced at a premium. 2 will be fair and one will be a bargain. It's completely worthwhile to buy one of those 10, even if it's at a slight premium. The cost of ownership really plays a big part in the overall cost of a Jeep.