@IronPercheron What year do you have? The motor on the pre '08 HEMI has a larger than nonexistent chance it will drop a valve. There is a gasket you can install that would mitigate the damage to the motor if it were to happen. It's very rare, but it's not unheard of.
There was a computer recall that tends to jack up the motor on the low-range transfer case (N23 maybe?)...
If the one you have has the Quadra-Drive (amazing system) you want to make sure that the diffs are services with the special ESLD additive.
Other then that, they have the pretty bullet proof chrysler 8.25 differentials, and a pretty bulletproof transmission (assuming proper maintenance).
The audio systems are pretty horrible, and annoying to upgrade, but that's chrysler's in general.
The door handles have a tendency to crack. Mine have, but they still work just fine. Some people say it affects the mechanism. I haven't seen that with mine.
I would have to say though, that more than all the little things above, the biggest annoyance has been aftermarket parts. It does share the powertrain and suspension with the WK Grand Cherokee, so there are lift kits and the like out there. But when it comes to most other mods you're pretty much on your own. There are only a couple established (see reliable) companies that have any mods for them. Though, that does pretty much ensure that your Commander will be like nobody else's.
There's a bunch of info in my build thread (in sig) if you care to see how i've started working on mine.
I will end it off by saying that I absolutely love my XK.