Well, let's take a look at that front suspension of an E39 - without knowing your specific model or production month & year, I chose a 540i automatic, 8/98 - http://www.realoem.com/bmw/showparts.do?model=DE63&mospid=47588&btnr=31_0264&hg=31&fg=05 http://www.realoem.com/bmw/showparts.do?model=DE63&mospid=47588&btnr=31_0246&hg=31&fg=10 http://www.realoem.com/bmw/showparts.do?model=DE63&mospid=47588&btnr=31_0255&hg=31&fg=10 http://www.realoem.com/bmw/showparts.do?model=DE63&mospid=47588&btnr=31_0257&hg=31&fg=10 Clunks can come from all kinds of things, including any variety of what's shown, you'll want to examine the front suspension thoroughly to be able to hopefully pinpoint the cause of the noise.
Any shaking under braking? Other rotating vibrations? Is the clunk felt through the wheel or only heard as a sound?
My bad, 02 530i. The wheels are all good. This sound comes from on top, like something tower need to be tighten down. But I had all that checked, twice.
Can you make it clunk just by bouncing the suspension while the car is parked, or do you only get it while moving? If it's high in the shock tower, barring something like a fairly obvious broken spring or spring perch on the strut, that would make me think upper strut bearing (part #1 in the 2nd diagram) or something else loose/missing related to any of those parts pictured. Does everything appear to be in place when you pop the hood? Swaybar links/bushings are pretty obvious clunk suspects. Did you replace parts 5, 6, & 12 in the first diagram? If you only did 5 & 6, I suppose 12 could be a prospect for a clunk, but since that's mounted to the front axle assembly/subframe, you wouldn't think it would necessarily sound like it was high in the shocktower. Any chance of a blown/broken strut insert? Although, if that was really gone, that corner would bounce when pushed, as the insert wouldn't be doing any damping.