I'm on my second E46 M3; the first was a 2002 6MT and this one is a 2003 SMG. I was apprehensive about the SMG at first, but now I love it, especially for a commuter car. My 2003 has just a little over 126k on it. Last summer I had to do the cooling system, and the water pump had some much play that the fan was almost going to hit the radiator. A few weeks ago I did the rear wheel bearings, as one of them was starting to make a little noise. The next big project will be new suspension busings, as the originals are shot.
Like any car, get the best one you can afford.