I didn't cheat and look at everyone else's before i compiled my list, but was gratified to see that pretty much all of my (admittedly pretty minor gripes) were already stated.
1)The lack of a mist wiper feature (I was wondering if it was only the 2003s, as my girlfriend's '04 Corolla has one(!) but i guess it's all of them. wtf Toyota?
2)Freakin' driveline clunk. I had mine lubed at the dealer when I got my oil changed and it quieted it for hundreds of yards. Drives me nuts.
3)The door unlock beeping. I am usually fast enough to get all 4 doors with just a 2-beeper, but it is still annoying.
4)Rear window no remote-uppie. It seems that it would not be difficult to program, if it is down the button puts it up, if it is up then the button puts it down, if it is in the middle, you have to manually attend to it.
5)No VSC off button. I have to admit this only bothers me in theory, as i haven't had snow to drive in since I bought my truck, but i am fully prepared to be annoyed with this. Not that i necessarily want to blow donuts in a vacant parking lot like I may or may not have done in my WRX

but it is occasionally a bit fun and/or necessary to be able to have the wheels getting the full dose of V8 goodness.
All these complaints notwithstanding, I still love my truck and its 18mpg and i can't wait for the first big blizzard to try out my Silent Armors!