Really hard to say as I put them in 2 different categories. I believe the 996 is a better drivers car in the end.

 

The 997 is about the same to 60 (4.6sec, iirc, lower for the 997S) and has a higher top speed, but the M3 will be a more practical and economical daily driver. The Porsche is better for at the limit driving, the thing is most people kid themselves about how much time they spend driving at that level; most Porsches are driven at levels that would make a Civic Si yawn with boredom.

 

996 all the way

 

depends if you want to use either one as a daily driver or not. speaking from experience (own e46 m3, best friend has 996C2), the m3 is the better daily and more of a gt than the 996. Can't go wrong with either one though really.