I've had pretty much all the problems others have listed on this site: windows falling into the door (twice!), wheel bearings, battery issues (when not driving car frequently though), catalytic converter broken -- does anyone know if warranty / recall will still cover this? I am just getting to fixing mine because the state my car is registered in (Florida) does not require inspection and I am looking to sell the car in NY/NJ.
I also had the moonroof / sunroof drains clog and flood the car, accessories break inside easily (though they look nice) and twice had the mirror cap fly off the car going 80 miles an hour on the highway... very dangerous and annoying.
I would say overall this car is more style than substance, though it has been OK over the years, as I have not taken the best care of it, partially due to the fact that every little thing seemed to cost me big bucks to fix.
My experience with the VW dealers has varied (It's been all over from Florida to California to Jersey to NY). On dealer did my 60K service, for which I paid some astronomical amount ($1,000), only several days later to have the car flood from clogged sunroof ducts. When I brought it in for another $500 fix and asked why they didn't check the ducts at the service, their excuse was that's not covered under the service package. Give me a break.
We are now getting rid of the car and buying a Subaru Forester (more room and more reliable). I still love the look of VW, but I'm not sure I'd buy another one -- maybe lease, but not purchase, because my experience has been a bottomless pit of fixes and expensive little issues.