I've never driven an S2000, but I've heard amazing things about it. That being said, there's something obviously very special about an M3. I am biased, but I think this especially applies to the E90 sedan. It is so much fun to hit the track in a 4-door "practical car" and not shame yourself among 911s, 370Zs, and Corvettes. And while the S2000 has a stratospheric redline even higher than the M3's, it's not a V8. The engine in this car is truly special, and most likely will not be continued in the future in the BMW line. Get one while you can.
Based on the above comments, the S2000 is very reliable and cheap to maintain. If this is a concern, just keep the M3 during the warranty period/free scheduled maintenance period.