I have a 2003 M5 and my driver's side window started to rattle one day when I closed the door. It became progressively worse until I started to hear a noise if I drove with the window cracked or all the way down, the only solution I had was to always close the door with the window rolled up, and not driving with it down.

The problem ended up being a bolt in the window slide rail that had backed its way out. There are two torx bolts that have the ability to do this. They are located a long the top of the door, one closer to the engine bay and the other closer to the trunk. The good news is if your problem is the one closer to the engine bay you do not have to remove your window glass. I had bad news in my case and was forced to remove it.

Tools needed:

• Screwdrivers
• Standard torx set
• Putty knife

Step 1 - Remove the door panel (This is brief as there are other guides on the internet)

1. Remove screw in A/C port in the upper corner of the door
2. Remove torx bolt in the center of the door handle
3. Gently pull the door panel off
4. Unplug the seat memory function if you have it, the floor light, and 2/3 window connectors. This should give you just enough slack to rest the door panel as if the door was in the closed position, and work with the door open.

Step 2 - Remove door glass

1. Remove the upper door trim from the outside and inside of the door. Starting on the outside simply pull this trim up. If you have trouble starting it use a plastic pry bar. For the inside trim pry up on the clamps until it pulls up.Back side of clamps
2. Gently peel back the bottom half of the vapor barrier (make sure not to tear it, and if you are careful you can reuse the old butyl tape to seal it back) and close the window about half way so you have access to the clamps that hold the glass in place. Back the torx bolts out enough so the clamps are loose on both sides.
3. 
4. Pull the window glass out the top of the window and set to the side.

Step 4 - Tightening the bolt

1. The bolt I had a problem with was the silver circle surrounded by the white collar(note door lock for reference point on door):
2. I was able to access it through here by barely removing the vapor barrier:
3. There is an identical piece on the door closer to the engine bay that can also be tightened without removing the window. You can try to source the rattling first to see which bolt is loose.
   

Step 5 - Reassemble

Put everything back together: window glass(then make sure it works), make sure your vapor barrier is sealed again, door panel, etc.