Just thought I would share my findings. My car had been doing this for a long time and I could not find the answer. I found a couple of long threads of others that were dealing with this issue but no one could really give a definate answer.

A couple of days ago I had some time to kill so I checked it out. As expected it was the brakes. What was happening was there was too much play up and down in between where the pads sat and the caliper. When I would brake the pad would grab the rotor and move in which ever direction it was going, since there was some space between the pad and caliper this would give it enough clearance to gain a little momentum and "clunk" against the top.

Now I don't think this would cause any kind of problems but the sound was very annoying. The pads sit on little metal pieces enclosed in the rotor, what I did was slightly bend these to get the pad a little more snug in the caliper and it seems to have worked (before you do this test the inner and outer pad by pressing it up and down in the caliper in the direction of the rotor. If there is some play that is more than likely your problem.) I have heard of brake hardware kits but I do not know what exactly is included. If they are the metal pieces that I slightly bent, only beefier, that would be a great alternative as I hear they are only $8.00.

After you reassemble make sure to torque the two caliper bolts to no more than 30ft/lbs or you'll eat up rotors. Give the rotor a spin after you are done before you put the wheel on, it should glide pretty smoothly, if not you have probably over torqued the bolts.

Hope this helps some of you that had these problems.