I don't know if this is too silly to be in here, but here goes anyway...
When I installed a pair of Bontrager metal fenders on my Shift, it turned out that the rear fender would bump violently into the frame, and the noise was especially annoying on coarse or rough surfaces. So I stuck a pair of felt tabs - the kind that goes on the tips of chair and table legs and the like - between the two to keep it all nice and quiet:
Problem solved.