Lots of things go wrong... But I do all the work myself so it isn't expensive.
Biggest problems:
Water in the fuse box! (bad bad bad)
Water in the trunk
Water on the floor.
All the drains work, and seals seem good, go figure?
Timing belt broke, but no damage occurs.
Drive-shaft fails
Struts don't last long
Brakes don't Last long.
Most of the problems occur because I really USE the car. I tow a boat with it. I drive it way too fast and too hard for a car this old, but she takes it in stride. This is a wonderful multipurpose vehicle (tow, offroad, fast, fun, good in snow) all around great car. There is nothing, not even new that is better. Reliablity has been good, but It has let me down twice in a big way (fuel leak, timing belt).
If you have a chance to get one DO IT! they are wonderful cars, soon you will find not just one, but two or three in your driveway.
The water gets into the trunk through the holes for (VW) and Scirocco signs at the back.
I've had this same problem with leaking through the emblems. A little bit of black silicon was applied behind them and they seem fine now though. I also had water in my fusebox that was fixed by cleaning the crud out of the firewall holes. You made some very good points about the problems. I thought they were random problems that only I was having.