For 1.8T's the individual coilpacks go out all of the time and leave the drivers thinking their car is going to explode, but it is a 30$ fix. Also make sure the timing belt has been changed. Check for cracks and such in lines in the engine bay, some of the parts are prone to cracking.
For 12v vr6's the chains need to be replaced around 100K, and the coolant distribution pipe on the front of the engine always cracks hence the name "crack pipe". The coilpacks do go out sometimes, but i dont know anyone who would pay $600 to have it replaced, the guy above got ripped off.
For 24v's the biggest problem is the slave cyl. and the coilpacks.