I had noises from where the interior panel met the steel door. VW put a very nice felt strip along the edge of the door panel where the two pieces meet, but unfortunately (like so many other things on these cars), their supplier used $h1t adhesive on it, and it doesn't stick so much as it makes a gooey mess. So in assembly, the felt shifted and left the plastic panel rubbing against the door. Pop the door panel, make sure it sits correctly on the edge, reassemble. I bought carpet tape (thin, white, double-stick) and will cut it into thin strips the next time I take the door apart and see if I can't make that felt strip stick once and for all. For now though, all is quiet.
Also, take a look at that rubber boot that is on the hinge side of the door (that the wires run through). The rubber is somewhat sticky, and will make a crackling/creaking noise when you open/close the door. Your problem may actually be there.