I was struggling with the "window rattle" problem for years as well. I tried lubing the window seals with both gummifledge and 3M "Wet" Silicone Spray. Neither worked well. Had a bunch of window regulators replaced at the dealership too. Whenever I cracked the window open, the noise went away, so I figured it had to be a window seal.
Turns out the window rattle wasn't a window rattle at all, it was a dirty felt door seal and an unlubed plastic strip at the very top of the door / door frame. Who would have known?!
The following DIY was originally posted on bimmerfest.com:
The window rattle is dirty door seals.
Assuming you have a 4 door sedan, open the driver door and stand between it and the driver seat, facing the door.
At the top left corner of the door, running across and down towards the door hinge is a door seal with a felt edge. That is your culprit. Clean it and lubricate with Gummipflege.
Now turn to face the driver seat and clean the black metal strip that the door seal seals against when the door is closed. Lightly lubricate it also where the strip meets it when it is shut. That should do it.
I copied this off of the Bimmerfest site, I had the exact same problem it sounds like you are having. This absolutely worked a miracle for me. No more popping over bumps and at slow speeds. Instead of Gummipflege from the dealer I used Sil-Glyde from NAPA p/n 765-1351 for $4.88 a tube. About a 2/3 cheaper than Gummi.
Give this a try.