A/C evaporator coil leaks. (A/C inop, dash must come out)

A failing Trans pressure sensor is common and will give a false reading to the PCM (44RE, 42RE, causing weird shifts, 1st-2nd gears)

The crank position sensors often fail at around 80K-100k miles, this usually also kills the data link connection from the PCM, because the PCM goes to self protection mode and shuts off until the shorted sensor is disconnected from the system and the PCM resets. (Can be easily confused with a failed PCM) The engine usually won't restart when it cools, or if it does, quickly stalls again.

PCM's sometimes fail (The engine dies and won't restart after it's hot, and may restart after it cools)

The door interior trim panel upper inserts usually peel, dark colors are worse.

The Trans cooler lines like to leak.

The trans output to t-case (4x4 Extension housing) seal likes to leak.

Water pumps fail every 3-4 years.

If it has a V8, the carrier bearings in the aluminum dana 44 rear diff like to fail. They will be noisy if they are worn. They need to be rebuilt by someone who knows the new TSB preload specs or the bearings will fail again in 10-20k miles if setup too tight like the original specs required.

The dana 35 rear axle in six cylinder ZJ's is weak, too. usually, they need major repairs by 100k miles, especially if the jeep was used for towing.

Those are the few I remember offhand.