Brakes. Front brakes especially. Turned to dust about every 10,000 miles. This seemed common to about half the GCL owners I knew. Finally went to lifetime brakes and rotors from Monroe - at least I only pay labor now.
Overheating. Early on (2003) the Jeep overheated because the thermostat went bad. My kids drove it on 2 or 3 occasions and that caused it to overheat very severely before we got the thermostat replaced. The effect (this was at about 60,000 miles) was that we picked up a "tapping" in the engine.
Tapping in the engine. This was, I think, caused by the overheating stress to the engine. It has been diagnosed as a loose wrist pin in the cylinder closest to the firewall. The prognosis was "the bottom end on a jeep might run for 500k miles, so you're better letting it go until it breaks than tearing it down to fix it". Happily, that diagnosis was about 160,000 miles ago.
Electric Fan. While vacationing in NC, we learned that the electric fan wasn't working when I left my wife sitting in the car with the AC on while I went into McDonald's. I looked out the window just in time to see her jump out of the car as steam was billowing out from under the hood. The radiator had burst. We replaced the radiator and eventually bought a fan blade and a fan clutch to mount on the engine (you can't order these new from the same place, because they all claim this car should have an electric fan - I got the clutch from Rock Auto Parts on-line and the fan from someone else). That's been working fine. It sounds like a 1970 V-8 truck when you first start out and the clutch hasn't kicked in, but it keeps the engine temperature very constant. Although I thought this would kill my gas mileage, it has barely affected it.
Water Pump. The problem that led me to this site was researching how difficult it would be to replace the water pump. Mine is bad now - leaking water like crazy - and so needs to be replaced. I was wondering whether or not anyone can tell me if the additional torque created by the engine-mounted fan caused a problem with the water pump. I'm guessing not since there is only one water pump spec'd for this vehicle.
Power steering. Last summer the power steering got a lot stiffer. I'm not sure what's causing that.
No problems with locks, backup lights, or most of the other things y'all are complaining about. I've owned this truck since day 1.