1) Fan module problems. The fan starts acting up, and will kick in at full rpm, making a horrible loud noise. Also can continue running while the car is off, or cease functioning completely. This is a simple replacement at the dealership under warranty.
2) Fuel Evap CEL's. If you buy a 2003, its possible the car hasn't received PCM updates, and can get CEL's based on erronous codes. The solution for this is a PCM update.
3) ATX issues: Harsh shifting and/or bucking. Two results. Either a) Your transmission is over heating or b) You don't have the latest PCM update which addresses the bucking issue.
4) Brake squeel/warped rotors/brake dust: Fixes for these parts are in the works and should be available now, or extremely soon.