I bought my first Boxster last week, and it had the rattle you described.
While yours could be one of a hundred different things, here's something that's quick, easy, and free to test.
Wrap 3-4 strands of electrical tape around the door latch striker then test-drive the car. If the rattle is gone, it means your door striker needs adjustment (a plausible cause after a major pothole strike).
This proved to be the case on my Boxster, and was also the culprit for a maddening rattle I had in the back of a Mazda Tribute. It's hard to troubleshoot, because the sound is nothing you'd associate with a door latching mechanism.
Good luck!
Here's another thread on the same topic:
http://986forum.com/forums/showthread.php?t=12553&highlight=door+rattle