I have a 98 boxster, that I recently got, and its quite unless I hit a big bump then I hear a clunk in the rear end, not loud, and I have been unable to find anything loose underneath, its not a noise unless I hit a big hole or crack, then its a clunk of sorts, could it be the rear shocks?

 

Could be the rear shocks, a control or trailing arm, or even the exhaust. Suspension noises are always a real pain to figure out...