I had a 2000 (e46) 328ci. The rear subframe was falling out of it... literally.
So if you look at one, absolutely make sure you look at the rear subframe where it's connected to the body of the car and check for cracks and metal actually pealing from where it's bolted to the subframe. A lot of people don't know, but this was a recall in Europe and completely ignored here in the states.
http://forum.e46fanatics.com/showthread.php?t=195602
http://forum.e46fanatics.com/showthread.php?t=679669
I told BMW of North America that I knew about the recalls in Europe and they fixed the car at 0 cost to me. As in, they welded a brand new subframe into the car for free through a dealer, who had to send it to a BMW approved body shop. ($$$$$$$$$$$$$) The car had over 100k miles on it at the time.
Also, the blower motor may have a mind of it's own, needs a capacitor pack replaced if it does.
Other than that the car had 120k on it when I traded it in. Nothing really wrong with it. Needed shocks and brakes, that's about it.
E46 M3 is one of the best looking BMWs to date if you ask me. The E39 M5 is a very close runner up.
Edit: In case you don't know..... If you are looking to track it a lot and not street drive. You might want to look for an E46 M3 CSL. It's lightened and doesn't come with a radio or A/C.