well its like this, the m3 makes a terrible roadster and the Boxster makes a terrible coupe. Get my meaning? You are giving up something to get the other.
They can never be compared as equals. A better comparison would be M3 vs. CaymanS. Although the new M3 is a substantially quicker car than previous M3's.
The Boxster is the only Porsche ever made to be a convertible from the begining, A 'real' roadster, not a coupe that had its roof hacked off. So when you are buying a Boxster you are buying a different sports car experience. It's like dating the girl next door vs. the Brazilian exchange student before she was discovered by Ford modeling. Coupes a great but a roadster is a whole new world.
So forget 0-60 times, long and lateral g's, HP's, gear ratios, etc.
The question is are you going to follow the herd or be a real man.