I had a 996 GT3, as well as an E92 M3, with both street and track experience with both. I'm not sure what your goal is, but these are just two very different cars, and hardly worth comparing. The M3 is one of the best sport sedans around, capable of comfortable daily driving as well as some sporty back road driving, and casual track use. The 996 GT3 may be the best value around in a real sports car, especially if you have some track use in mind. As a 911 platform car, it has handling characteristics that require some dilligence to master. But, if you put the time in, it is one of the most satisfying cars on the planet to drive. But, it is a car to be enjoyed by driving, as an experience, not as an exercise in transportation. As a daily driver, I would not consider it. As a second car to be enjoyed on track or a favorite country road, it is wonderful.
2011 Space Gray Coupe, DCT, ZCP, StopTech ST-60/ST-40 BBK.