You really can't go wrong with any used '97-'06 TJ Wrangler. The frames, engines, transmissions, and transfer cases are a great foundation to build a solid, reliable Jeep. But there are a few things to look out for, and we still have our favorite years and options.
For the most durable Wrangler per dollar, we'd put our money on an '00-'03 with a 4.0L and NV3550 manual five-speed tranny. It's easily a 250,000-mile powertrain combination if maintained properly. Of course, we absolutely love the performance of the '04-and-later NSG370 six-speed manual mated to the 4.0L, but we have reservations about the NSGs durability if larger tires and more power are planned. The 3550 is an extremely durable (albeit noisy) truck transmission that can be found in 1/2-ton trucks with V-8s. Needless to say, it's certainly overkill (the good kind) when used in a Wrangler. The '99-and-earlier AX-15 is a decent transmission as well, but it doesn't compare to the 3550, in our opinion.
None of the automatics Jeep has used in the Wrangler offers impressive performance, especially with larger tires. So we'd pass on the auto unless your left leg is incredibly lazy and you don't mind a sluggish Jeep. Obviously, if you plan on tearing out the drivetain to swap in something else, then it doesn't matter what powertrain combination you start with. Although, you'll be able to recoup some of the swap cost by selling off the 4.0L engine and its components because they'll generally fetch more coin than their four-cylinder counterparts.
The '00-'03 TJs come standard with the NP231 T-case and a reasonably durable Dana 30 front axle-plus, many are optioned with the desirable Dana 44 rearend, as well (look for the stop-sign-shaped diff cover). The Dana 35 rear axle found in many TJs is the only real fly in the soup. If your TJ came with a Dana 35 axle, it's best to avoid the temptation to modify it. Your money will be better spent on a swap if you want gears, lockers, and so on. While the more expensive Rubicon models come with Dana 44s front and rear, most people may not need the traction that lockers front and rear provide. Also, the Rubicon's 4:1-geared NV241OR can be a bummer if mud, sand, hillclimbs, or any other off-roading involving more wheel speed is encountered.
If you like slow-speed, technical trail driving, then by all means, keep an eye out for a Rubicon model. But also keep in mind the axles are only marginally better than those of the standard TJs. Weak axletubes plague Wranglers and Wrangler Rubicons alike. And the Dana 30 and 44 front outer-knuckle assemblies are interchangeable between the two, so there's no difference in strength or durability. The only real gain in strength is in the ring-and-pinion.
The Sport and X models are good buys. The Sahara is typically too optioned-out for our tastes, and the SE is generally too stripped and is frequently found with a four-cylinder. Not that the four-poppers are bad, it's just that they don't compare in performance to the 4.0L. Also, don't fool yourself into thinking the four-cylinder will have plenty of power if you really don't feel that way. One of the most common questions we get is, "How do I put a 4.0L in my four-cylinder Jeep?" And the best (least expensive) answer is always, "Sell it, and buy a 4.0L Wrangler." Aside from a turbo or supercharger, four-cylinder power modifications will be unimpressive, as well.
Purchasing an already-lifted TJ can save you some money or provide you with someone else's headaches. If you have to have a lifted TJ, choose a Jeep with a complete suspension lift kit (including a slip-yoke-eliminator kit and CV rear driveshaft) rather than a thrown-together combination of parts and spacers. It's really hard to hide off-road damage and abuse, so look for gouges and dents in the skidplates, mud packed into the frame, and so on. A Jeep with a clean, straight underside is worth more than a beat-up one, so adjust the price accordingly if you're looking for a built, seasoned Wrangler. Steer away from anything that looks like it's been slapped together with a home-welder and scrap steel.
Like nearly all Jeeps, Wranglers have been known to have a few leaks. Inspect Jeeps with over 85,000 miles on them very carefully. Common leak locations are the 4.0L rear main seal, radiator seams, and the NP231 rear output. A leaky rear main isn't a big deal unless it's really leaking a lot. Too much oil on the clutch will cause it to slip. A few drops are nothing to worry about and are fairly common for high-mileage 4.0Ls.
If the T-case looks like it's leaking a lot (the underside of the Jeep is dripping with light oil), then you should check the T-case oil level. If it's really low or filthy, then you should move on and find a Jeep that's been properly maintained or adjust the price accordingly. Low and dirty oil in the NP231 will kill it.
Wrangler radiators feature plastic tanks. The seam between the core and tanks will often leak on high-mileage Jeeps. Pop the hood and look for coolant and seepage residue around the tank seams.