BMW parts depts sell a teflon-based lubricant in a small squeezy bottle that you can treat the seals with. This cures a lot of the squeaking you'll hear. Failing that you can buy silicone spray from Halfords.
Normally the top of the windows that cause the bird sanctuary type noises, try dropping the windows with the roof up and see if they go away, then your know where to lube up.