As jay had mentioned the boxster s not only receives better better brakes, a 6 speed, the 3rd rad, ect.. The boxster S also receives forged pistons. And either forged rods or crank.
I've driven other boxsters and I think what really drew me in was the 3.2. That being said I think when Porsche designed the boxster they ended up with a better platform than the 911 but were to proud to admit it. Hence why the base 996 got a 3.4 and S got a 3.2.
But you know... a little idea in my head about doing a 996TT swap or GT3.. help pls