Door Dope
The, ahem, unique design of the inner fender/door area where the hinges can be seen from the inner fender is often problematic. The factory installed a flimsy piece of closed-cell foam rubber in the fender and inner fender plastic to prevent kicked up dirt getting to the hinges, wiring, and door-strap. Dirt in this area can cause the door-strap to seize, the hinges to wear prematurely and possibly damage the wire. Many of us remove those plastic liners or modify them when we cut the fenders, leaving an opening for dirt to get in. The closed-cell foam falls out more than it stays in and many XJ owners don't even know about it. It all contributes to problems down the road.
Prevention: Leave the plastic inner fender liner in-place and make sure to clean and oil the hinges and door-strap after wheeling trips if they get dirty. Check that your rubber wire loom going to the door is attached at the door and body and has no rips or tears.
Cure: Leave the plastic inner fender liner in place or use a pool noodle jammed between the inner and outer fender. Google pool noodle if you don't know what one is, but one noodle will usually do both sides of the Jeep, and with some trial and error you can get it to fit in there really tight and keep more dirt away from the door than the factory ever did.
Top Shock Shatter
This is another example of a brilliant engineer/designer getting beaten by good old Mother Nature. The top mounts for the rear shocks are captured nuts. Makes them real easy to install if they work correctly but a seemingly small amount of oxidation can make the bolts non-removable. How do you know if they are non-removable? Glad you asked. You find out when your 3/8-drive ratchet with extension and 13mm socket suddenly break loose and your knuckles end up in the exhaust or the gas tank. The crux of the matter is that the "captured" nuts are really more like "lazy" nuts. They just lay on the top of the crossmember; they aren't in a box. So, every time you go wheeling you get a little more dirt up there. Dirt attracts and retains moisture. Then you've got a great recipe for seized bolts.
Prevention: Make it a point to get up under there and get as much dirt as possible out by sliding your air-nozzle on top of the crossmember and blowing it out with compressed air after each wheeling trip. Use anti-seize when installing the bolts.
Cure: Once you break the bolt, you have two basic options. Either drill the captured nut out and re-tap it or punch it out with a hammer, slide a bolt in from the back side, and tack weld it from the bottom.
Fishbowl
This is an area you might never see, but the very first time we pulled our trim panels off, both sides were filled with water looking very much like a metal fishbowl. We thought about putting some guppies in there, but then decided to figure out the problem. By tracking the water trails, it turns out that the rear quarter window seals don't seal quite well enough. The water gets past the quarter windows, drips behind the trim panels and right into the rear lower quarter panels. The water normally doesn't get onto the carpet, and doesn't create any mold smells so it often goes unnoticed. However if your Jeep has this ailment, it is only a matter of time until your quarters will rot out. The water will always find a way out.
Prevention: Either pull the drain plugs located on the inside vertical face of the fishbowl or drill a small hole through right at the bottom and above the pinch seam. Too big of a hole will let mud and dirt in, too small will clog very easily. We use a 1/8-inch bit normally. By drilling the hole, all the water gets out, not just the top three inches' worth.
Cure: Pop the quarter windows out and reinstall with some RTV. We like using Right Stuff, but any kind will do. On the downside, if (when) you smack the rear quarter panel, instead of popping out, the window will likely break. On the upside you keep the water out.