I have an 1998 540iA that has 143,000 miles on it. When i do hard braking I hear clonking noise coming from the brakes maybe? I have taken the rear brakes off to the hub, I can't find anything. I have replaced the sway bar end links,rear control arms, bearings, rotors and pads. I also here the noise when I take off from a dead stop....If this has already been covered please point me to the right direction. Thank You.

Did you ever find out what that was? My car is doing the same thing...

Shocks going bad, maybe they're bottoming out??? Just a guess

You didn't mention subframe bushings:

http://www.meyleusa.com/33%2031%206%20770%20454%20X5%20Rear%20Subframe%20M ounts.jpg

Shocks going bad, maybe they're bottoming out??? Just a guess
Well, it doesn't make this noise over the bumps or when I "bounce" the car. Only under acceleration or braking it makes a "tap" sound, once in a given direction. I'm going to look at the sub-frame bushings. I can just support the whole assembly by the diff while I unbolt them,right ?

LOL! IT just might be the tiny bit of free play in the brake pads when they sit in the caliper. You apply brakes and the free floating pads come in contact with the rotors and they shift the 1mm and tap the caliper housing that holds them. Then from a standstill the rotors will move the pad in the other direction and "tap" it's backplate against the caliper housing again. It's funny that you did so much to eliminate this noise and yet this is all it is.

Remove your pads and clean the caliper and pads with brake cleaner. Clean well. Apply the silicone brake pad "butter" very liberally on ALL surfaces that will make contact, even the sides of the pad backing plate. Let it set for 10 min then re install.

Or you could just live with it, knowing what it is.

BTW, i know because mine does the same thing after i did the brakes. I pulled them apart again because i forgot to apply the butter. Afterwards they were whisper quiet as the adhesive held the pad in place. But because the adhesive sucked it let go within a week and the tap started again. Now i learned and bought the thick silicone type in a squeeze bottle and NOT the single use shiat in the metal pockets.

Now i'm waiting till i feel like pulling all the calipers AGAIN. I just threw up in my mouth at the thought.

Well, mine turned out to be the rear ball joint sliding back and forth inside the carrier.