Have you replaced your brake pads recently? If so, did you use OEM or aftermarket replacements? I had this exact same problem on my '01 325Ci, about 500 miles after I replaced the front brake pads with Akeebonos. Took it to my mechanic and he suggested getting a replacement pair and give it a try. I contacted Akeebono and they sent a free replacement, and the problem is gone after I changed them.

Akeebonos are great pads, and they meet OEM specs, so I am not suspicious about them, I think it may have been a bad batch or something. I replaced the pads on both sides, but I was only getting the "clunk" from the front passenger's side.

Hopethis helps.