I have always wanted a Jetta and finally was able to afford a loan and purchase one in February of 2005. The transmission always felt kind of funny from the beginning, like it was slipping. It still feels like that today but nothing too bad. I've been told that the transmission fluid is "factory sealed" and is a total pain to find someone who can change it, as I'm sure that might help.
In late 06/early 07, I had a major oil leak. I'm talking a quart or more a day was pouring out. Finally took it to get fixed and was told it was the oil sending unit, and it was only a $30 fix. Awesome. No problems with that since but I do notice things to be a little greasy looking under there again.
In December of 07 I locked the doors one night before leaving my car and then they wouldn't open. Had to call a tow truck to open it, which sent it into security alarm mode, which killed the battery. What a nightmare. They just plain old don't work now. The trunk only selectively opens with the power button inside too.
The side panel on the passenger side is just starting to peel off now. I've noticed ALOT of these cars have those strips missing. No big deal. I'm not that vain. A little gorilla glue and I'm set.
My BIGGEST problem with this car is that it doesn't like to start and/or run in the rain. Apparently I'm not the only one with this problem. Stalled a few times if I went through a huge puddle or something but I figured "hey, my fault, probably shouldn't be going through big puddles". It only got worse. Took it to a few different garages and called the VW dealership in town and everyone either had no answer or a different answer, and I wasn't trying to spend money on 100 different things to "find" the problem. It got so bad that it wouldn't start if it was humid, let alone raining. In June of 07 I got a full tune-up. Paid $160 for it, which I was told was cheap for that car. Ran OK for a while but then started the same old crap again. I've had to miss countless days of work and important events, not to mention the embarrassment factor. Like so many others, if and when you do get it started, it chugs and sputters and will stall at the drop of a hat. Ridiculous. My car also does that thing where it sounds like it wants to start after you put it in the off position and makes a loud bang. Eventually it usually does but this is an on-going SUPER annoying problem that I just can't seem to find an answer to. The car is a 96 and only had 62,000 on it when I got it in 05 and only 93,000 now.