Things went wrong since I have had the car:
Shadow line trim started to corroded on both rear doors. Car was under warranty, and was replaced no charge.
Had a flood in the rear floor. Took 3 days for BMW to figure it out that it was the weather barrier on the door that came loose, which took me 5 minutes to figure out. Fixed under warranty.
Radio had a weak reception, bulletin was out to replace the head unit, covered under warranty.
When I got the car, the 12v power outlet was dead, they fixed it under warranty.
One of the Key fobs went dead, car was under warranty and they replace one of the keys.
Cup-holders, well, lets just say are as good as not having one at all and just using the dash top. Any turns will cause the drink to fall out, or its too small to fit anything. Ummm shot of espresso would fit...
Audio system, on a non-dsp vehicle, let just say, is very weak, shame for a vehicle of this class. But the system is very easily up graded, if you have some experience with mobile audio.
I am a DIY type of guy. Actually when I do work on the car, it a pleasure since the E39 is put together so well. Thank God it was still covered when I first got the car. I think if you maintain this car, it will last a long time. Plus it was the last model with no i-Drive. It's a keeper.