Well I have no experience in driving them in a Boxster, I have driven them in the 911. Both engines are quite a step up from my 2.5! the major boost being the noticeable low end torque. Between the two engines, the increase in torque from the 3.6 motor seemed to be huge. They are both very good motors, I can only imagine them in a boxster, but I would say, if you are doing a swap and you could afford the 3.6, you would be stupid not to. Eh, for that matter, just drop in a x51 3.8!
Steve