They are overall fairly good trucks. The biggest issue is finding a solid one that hasn't been modded incorrectly or been run into the ground.
Bottom line they are solid trucks. Keep in mind the are kin to a Defender 90. Not the most comfortable vehicles out there so don't get all pissy when it doesn't ride like a caddy or even as well as a chevy malibu. However they do bring the win off road as well as the chicks dig em.
100k the clutches have issues. They have internal slave cylinders that bring all kinds of misery.
The 4.0 is bullet proof for the most part but I haven't seen one get to 200k yet. Close, but not yet.
The 5 speed transmission is solid, both the AX-15 and the NV3550. The later NSG 670 6 speed appears to be reliable in the TJ (not so much in the JK).
The suspension links are shit. You start off roading, you will break them. Also the suspension geometry starts sucking once you try lifting it anything over 2".
The rear axle is a ticking time bomb unless you get the TJ sport. The normal TJs are equipped with the Dana 35 axle. Kept open, babied, and not going nuts with tire size, they generally last. However they are typically replaced rather than built. Not a favorable axle. The TJ sport was optionally equipped with the Dana 44 rear axle which is very reliable.
The front axle...meh. It does the job. Start throwing 35s under there and you'll go through ball joints, wheel bearings, and U-joints. On the front axle, if you break a U-joint, STOP AND REPLACE. If you drive it, the remains on the U-joint will kill the axle shafts.
The transfer case is ok but has the slip joint built into it. Off road with a lifted suspension, you run the risk of pulling the rear driveshaft out of the rear of the transfer case. A ~$250 kit fixes this.
Another big issue is when the front driveshaft gets bent. It kills the pinion bearings QUICKLY. This sucks.
The roll bar works, but there is NO protection around the windshield. You might be tempted to buy a kit to fix that. I haven't seen a single one of those kits actually work in a roll over. You want A-pillar protection? Cut the dash and put some tube to the chassis.
At around a 33" tire, the stock tire carrier really starts to stress the hell out of the rear door, especially off road. Anything bigger and you need to get a bumper mounted tire carrier.
Pull the rear seats to get some actual storage space in the rear. If you go topless (bikini top, more likely) get a duster cover for the rear. Very popular and typically work pretty good. However the rear seat is fine for a 5' 9" guy for short trips. You definitely have the "wind in your face" feel back there. Also driving around with the doors off on a TJ feels right.
ALWAYS CHECK THE LUG NUTS!!! Torque them properly and then check them later!!! When the driver front tire (yes, that is THE ONE that comes off) leaves the vehicle, it is a big issue. Also it pisses off the rest of traffic.
The power steering boxes don't last forever. When it goes, find a GOOD QUALITY NEW replacement. Don't bother with a rebuilt...unless you love installing PS boxes.
Damn track bar bushings ALWAYS go out!! Then you have death wobble and it is miserable.
Also on that, look at adding a steering stabilizer. Seems like adding this makes a huge difference in steering.
The auto trans works ok but the early 3 speeds leave something to be desired. Put a cooler on it and all should be fine.
Assuming both are in good shape, heater and AC can keep up as long as the cab is enclosed.
Noise isn't that bad until you take out all the interior and add mud tires. Usually the stereo can keep up. Unfortunately the stock speakers and head unit aren't "element resistant". Get some mud in those speakers and it goes downhill fast.
The hoop set is easily damaged off road and then it sucks when trying to put the top back up.
Seems like if you go off road, you gotta carry a crap ton of spares...and use them.
LOTS of torx bolts on the truck. Brace yourself.
Bottom line, they are an ok truck. Lots of little issues that can be eventually massaged out but really it seems like they are another rover. Constant attention and constant issues. Of course I am referring only to modified/built vehicles. Stock is another story. Take the top and doors off and go cruise. It feels good. Those are my thoughts on the TJ.