In chronological order:
Headlights, approx. about 8 in 8 years. Dealer replacement cost is about $75. Tried having independent mechanic replace it once, and he broke the mechanism because it's unusual and hard to replace.
Catalytic converter and 02 sensors. Replaced once at about 92K, was told wasn't covered under warranty. Cost to replace was close to 1K. Then later there was a warranty extension, and I submitted a claim and VW paid for the CC but not the 02 sensors. The toll on me coming up with the $ to get the work done so the car could pass CA smog and get re-registered was substantial. Then at about 130k check engine light is back on and it looks like I need new 02 sensors, mass air filter and possibly cc again. The cost will likely be around 1K.
Timing belt, water pump replacement, all belts and hoses replaced (this is all normal maintenance). I did it at about 120k, but it was supposed to be done about 100K.
Brakes (needed new rotors because I waited too long.) Then just had brakes done again.
Tires. I'm on the 3rd set of tires I believe.
Window regulators, both sides, replaced under special warranty recall thing.
Inside electric mirror switch replaced.
Driver's exterior door handle basically fell apart and had to be put back together, cost was about $200.
Fuel pump, fuel pump, fuel pump cable all had to be replaced recently.
Ignition coil (this is a black box) had to be replaced, this was about $200 for the part.
Horn started beeping by itself when making turns, haven't had it fixed yet, I pulled the fuse instead.
Fan motor (for ac/heat etc) stopped working, haven't had it fixed yet. Hope the AC is OK.
Interior door handles peeled.
Paint on interior doors peeled (but heavy use). Think it's a bad design to have painted surface on interior as its susceptible to scratches, peeling.
Engine head was taken off, re-machined and put back on with new gasket. (Done by 3rd party mechanic.) not sure what happened to it, could be from loss of oil or overheating or both.
Oil pan got stripped at oil plug thread, this is a common thing that happens because pan is aluminum, plug is steel, and some fast mechanics use air wrenches too strongly. Haven't had the pan replaced yet, 3rd party mechanic put in bigger plug, not sure if this is a viable fix. This happens to other model cars also.
Electric hatchback release switch stopped working.
Both keys/fobs had the metal hook that goes on keyring crack off because part of the key in that area is plastic, it's not solid metal design.
Electric gas cover switch stopped working.
Top of center console between seats cracked off.
Cloth seats have wear, driver's seat has small tear.
Rear headroom is bad. I didn't know this when I bought the car. Rear seat is basically unusable by adults. If I had known this, I probably would have bought the Golf instead, or maybe a different car. I assumed the VW designers made enough headroom for adults to sit in back, I was in a rush buying a new car (when old car died) and I don't think I sat in backseat to check it out before buying. I had a 67 Bug and rear headroom was OK. Also most normal cars have OK rear headroom, so it didn't occur to me that VW would be stupid enough to design this car with inadequate rear headroom. I read they are going to fix this in the redesign for 2012.
I looked at photos of the original 1939 VW Bug and noted that it seems to have been designed with good rear headroom. The bad rear headroom is unique to the stupid redesign of the New Beetle not the old Beetle design.
My feelings on the car are mixed. I think it has been only so so on reliability, and has some problem areas with electrical things. Also the engine has greater oil consumption than typical. When I bought the car I assumed it was a quality car made in Germany. Then later I learned it was made in Mexico (I think.) If I knew this I would have inquired which of the VW models are still made in Germany and would have tried to buy one of them.