I could be wrong but I think this post may belong under the relatively newly created Q&A Porsche Discussion section. As a result, I am afraid all of the responding posts will soon be eliminated but I think from at least a performance comparison it depends on which M3 you are referring to.
If you are referring to the E36 that was produced at the same time as the 993, then the 993 has better performance. For anyone interested there is a magazine scan that tests these two cars along with others by Car & Driver at
http://www.motorworld.net/forum/showthread.php?t=12004
If you are referring to the current E46 then the I believe that the performance is basically the same.
The thing I like I like about the M3 is the practicality of a sedan combined with the performance of a sports car. It is like two cars in one.