That happens to be a common fault with E39's.
It has something to do with the door seals, so say the BMW community.
Personally, I traced mine to the plastic door sills.
Try pressing repeatedly on the door sills and see if they make a squeaking or creaking noise.
If they do, or sound like what you have been hearing (sounds like old ship creaking when the sails are turned hard!) do this:
Carefully pry up the chrome/rubber door sills. (Don't break any clips)
You pry one end and slide (backwards, I think...)
Then holding the whole door sill in your hand, you're able to analyse it better.
Separate the chrome and the rubber pieces.
Apply grease in between the clips and joints, and anywhere that rubs.
Apply grease as well around the holes on the car where the door sills clip onto.
Re install the door sills. It should at least be quieter now.
What happened in mine was when the car moves esp at slow speeds,
the doors (and rubber weather seals) flex and move, and rubs, or press against the door sills. When I was researching, everybody said it was the rubber seals...I didn't think rubber seals would make creaking noises!
But fixing the door sills eliminated my problems permanently...until about maybe 2 years later, when I started to hear a little of it. Probably time to re-grease then.
Note: This solved the problem in my car, and I believe it is the solution to most of the squeaking doors in the E39. However, this is just my opinion. It might or might not help solve yours, but there's no harm in trying it out.
Last edited by CosmosBlack; 12-05-2006 at 11:54 AM.