The water pump failed "prematurely" according to the dealer. The coolant light did go on, but the temperature gauge never climbed - and I could tell the car was starting to run hot.
The air conditioning failed. There was no refrigerant left in the system - the dealer couldn't find a leak and suggested that perhaps "they didn't fill it up all the way when they built the car". It seems more likely that there's a bad seal somewhere that's small enough that it can't be detected with the dye they shot into the system, but big enough that in another year, when the car is out of warranty, it'll run dry again.
The door locking pin rattles and buzzes on the driver's side door. The dealer has tried to fix this several times. First they removed the door panel and found a loose retaining clip. No difference. Then they tightened the latch on the door. No difference.
The seats have fabric that grabs lint and dirt from clothes and hangs onto to it unless it is very carefully vacuumed. I understand that Volkswagen has switched to a different fabric.
The right front passenger side door speaker buzzes with the volume turned to a very modest level and no extra bass or treble added.
Although I really enjoyed the car and found it spacious, sporty, and priced right, the problems I described above, combined with the stories I know from friends about failed window regulators and the short Volkswagen warranty on 2000 models scared me enough to sell the car.
I have a friend who owns Volkswagens and she told me that if one gets a bad model in a particular year to get rid of it - "You won't believe how many things can keep going wrong". Good models in good years are great, she says. I bought an Acura CL-S Type S and know from owning an Integra for 7 years that it'll likely be trouble-free.
One other comment: VW service departments are overloaded with repairs. The two dealers I called for an appointment each told me that the next available slot was a week away, even though I told them the coolant light was on and the car was leaking coolant. In the meantime, I had to go without my car and without a loaner. Parts were not in stock and delayed the repair another several days - at which point a loaner car was offered.
A Volkswagen salesman I spoke with when I accompanied a friend to a dealership where the friend was buying a 2001.5 Passat told me that the Pueblo VW assembly plant ramped up production too quickly in 2000 and 2001. From 50,000 units to 250,000 - and that some of the problems stem from this decision. Golfs were moved to Brazil for assembly. Beetles are being held at 50,000 units. He thought they were scaling back on the number of Jettas being produced until the quality could be brought up to a better standard. Food for thought!