Based on what other boxster owners have reported, the spherical bearings in the rear track arms are pretty notorious for making clunking noises when hitting a bump at the rear wheel, after they get sufficiently large miles on them. Because I don't see why a similar problem couldnt happen at the front suspension (the front boxster suspension is basically the same design as the rear, but just a little lighter duty), replacing the front track arm would be my first instinct as to what you might try to fix your clunking noise.
(Alternately, you could try repairing the spherical bearing using this "peening" procedure - but of course, on your front track arm instead of the rear:
http://www.renntech.org/forums/topic/20681-boxster-control-arm-repair/ )
IME, the rear track arm clunking noise won't happen if you are dragging the brakes or accelerating while you hit the bumps - so something else you could try to learn about your problem better would be to try dragging the brakes lightly while going over bumps that you'd expect to make the noise, and verify whether dragging the brakes prevented the noise from happening.
Strut mounts probably wouldn't care whether you we're dragging the brakes or not. Ball joint noise might be quieted if you varied the lateral force (e.g., cornering or driving on a banked surface), but could respond to brake dragging also. Track arm bearings might also make noise regardless of lateral force (although I haven't tried that test yet on my clunking rear, I might have to now!). Steering tie rod end noise should also not be particularly sensitive to dragging brakes, assuming your suspension is not too badly engineered or tampered with (scrub radius isn't too badly out of whack).
Edit: here's a YouTube video showing the front "track arm" replacement procedure:
https://m.youtube.com/watch?v=899_OjGjBMg