well, i'm kinda stumped. this is really weird.....does it only happen when your moving or does it still happen when your stopped? if it continues while your stopped then it might be an engine trany problem.
if its only when your moving then it could be a few things. if you have disk brakes they could be warped,
loose tire(is there any wobble in the jeep? if not, then nevermind, but it could just be on 1 tire then there prob wouldn't be much wobble),
suspension could be loose and constantly shifting(however, that wouldn't really make a clunking sound and it would be less noticable. so prob not this.),
or something could be hanging down and hitting some moving part of something like that.
so,make sure lugs and suspension are tight, check under the jeep for hanging things. but if it happens while your not moving(just running in idle) then you dont need to check all that, it will be more than likely an engine or trany prob.
good luck and keep me updated