Cigarette lighter blew fuses. (Fixed twice under warranty.)
Electric sunroof inoperable (Fixed twice under warranty).
Intermittent wipers no longer function (Fixed once under warranty and then it happened again at 25k miles and I haven't gotten it fixed).
The horn periodically went off by itself (40-50k miles).
The tray under the passenger side front seat broke when my friend tried to move the seat up (5k miles).
The front fog lights filled with water, burned out, and now have rusty water in them (45k miles).
Door trim fell off (30k miles and 60k miles). It makes it look like a hooptie.
The driver side alarm became inoperable. Now I must open the car from passenger side in order to set and unset the alarm (60k miles). There must be a short somewhere, because I checked the fuses.
I had to have the front rotors replaced (50k miles) in order to pass inspection. The brake dust buildup on the front wheels is insane. I checked and Volkswagon doesn't recommend using ceramic pads.
I'm glad to see that there are others that experienced the same problems with their Jetta's and it's not just mine that is a piece of crap. This was my first brand-new car and I will never buy another Volkswagon.
Overall, I'd say that the electrical system is the biggest issue. My car was assembled in Mexico so perhaps that was the problem.
I also agree that the front cupholders were designed to hold espressos and not american coffee. And the glovebox belongs in a Porshe, not a four door sedan. The final issue I have is with the wheels... it is really hard to change the tires. Since the bolts come completely out, you have to have three hands to line up the wheels and put in the bolts.
In short, my car has under 65k miles and it looks and runs like it has 165k miles. I'm only keeping it because it's paid for and no one in their right mind would pay me the blue book value for it.