Clicking is probably a very broad problem, so i'll try to be as specific as possible. I've taken my jeep offroading plenty off times, so I won't be surprised if that's what caused this. It doesn't happen if I haven't been driving my jeep for at least 20 minutes, but when i'm sitting at a stoplight or at a drive-thru my jeep will start making this clicking noise at idle, but I discovered that when I press in the clutch pedal, the clicking disappears, sometimes I can even coax it into not clicking if I slowly release the clutch after pressing it in. I really hope this isn't a transmission problem, but it seems to be leaning that direction. Anything helps!