For the most part most of my problems have risen from the dealership I purchased the car from not repairing things to the car they were obligated to fix when they sold it to me, but here's a few of the things that have happened in the last year:
The water pump failed within days of me purchasing the car. The extended warranty I purchased covered it, but not any of the hoses or the flange that needed to be replaced as well.
The button to turn the dome light on and off by the sunroof broke.
The transmission needed to be replaced. It kept shifting hard between 2nd and 3rd gears (I notice that's a very common problem with this car). At first it sounded like the tires would chirp between gears... then it progressed to a hard "think" with the car jerking forward. Then the car would die if you shifted it into gear right after starting. Finally the car just wouldn't go...
The brake light module or something was recalled. It was fixed at no cost to me by the dealership (one of the few times I didn't have to pay for something)
The latch on the center console is broken... again a common problem with the early 2000ish Jetta's in general.
Most recently the auto-adjusting rear-view mirror has started to stop working. It normally turns a greenish color at night to dim headlights behind you. The bottom of the mirror no longer changes.
The charging system is AWFUL! If you let the car sit for more than a few days it refuses to start without a jump start. It may be because of the extra alarm system I have, but I know from friends who have owned Jetta's that the charging system is weak.
The rear power windows are starting to go out, but I will have the modules replaced as they are under a current recall.
Depending on the car's mood the information display in the instrument cluster will at times be illegible. This mostly happens during the daytime (the screen underneath the speedometer that tells you how many MPG you are getting, the exterior temperature, etc...)
At times the exterior thermometer has deiiferent readings for different screens. The screen in the instrument cluster can say one temperature, and the screen for the exterior temperature on the climate control system can say another.
The leather interior has a smell that is somewhat reminiscent of a box of Crayola Crayons...
As far as performance goes this car is awesome! It handles very well. Once I had the water pump and transmission replaced it drives like a brand new car.
The paint has held up very well for it being a 7 year old vehicle. It still looks very good.
The safety system is great. Unfortunately I have seen and felt every airbag that is available on this particular model and I am here today because of it. I bought this particular Jetta after I was involved in a major collission in my last Jetta. The airbags and seat belt re-tractors saved my life. I will buy a Volkswagen again for sure. The "Safety Happens" commercials are no joke, and they hit pretty close to home with me.
The cup holders are in a rather odd place. It's in a surprisingly strong yet delicate looking contraption located directly above the stereo system in the dashboard.
For having an 8 speaker Monsoon stereo system in the car you would think it would sound fantastic... but even with the equalizer changed around the car has very little bass sound and lots of treble. It takes a lot of tinkering to get it to sound manageable.
The dual front heated seats are a very nice feature. They heat up very quickly and feel great. Combined with the Lumbar supports it's a god send on a long road trip.
The "rain sensing" windshield wipers sometimes feel like they need contact lenses. They can't always keep up with the rain, and sometimes you have to resort to just flicking the speed selector back and forth manually to get a good speed.
Finally...the car alarm just sounds wimpy. It's a disgrace. The actual horn to the car is MUCH louder. I don't know why they didn't just hook the alarm up to the regular horn. The car alarm sounds like an underpowered VW Beetle horn. Like Herbie the Love Bug on downers...