I have found the source of the annoying whistling wind noise associated with the driver's side mirror in my '98 A4 2.8 and I have come up with a permanent fix. On my car this noise was at its worst at 65 MPH and above.
I kept trying to locate the source of the noise by placing electrical tape over various gaps until I finally found it. There's a black fairing that covers the mount between the driver's side mirror and the lower front corner of the driver's side window. Where the fairing meets the glass it is triangular in shape, with the "rear" portion vertical. On my car, there was about a 1/8 inch gap between the back vertical edge of the fairing and the window glass. When I covered that gap it stopped the noise dead.
I came up with a simple permanent fix, as illustrated and described in this FAQ. Before you go to the trouble of implementing this fix, I suggest you first try a test on your car by covering the gap with tape and going for a test ride.
Here's the permanent fix:
Go to a hardware store and buy a 4 1/2 inch long piece of 1/4 inch
diameter (OD) plastic tubing. The stuff I used was clear and had pretty thick walls, which is good. Black would be fine, too, but thin-walled tubing like drip irrigation line might not work as well. It is such a small piece they'll probably just give it to you for free.
Take an X-acto blade or razor blade and slit the tubing lengthwise along one side. Roll down your window and slide the slitted tubing over the back edge of the fairing. Close the window and work the tubing over so it seals the gap between the fairing and the window. Click here for a picture showing the installed fix.
That's it. It doesn't affect the use of the window and should last the life of the car. If the tubing slides up and down a bit you might need to squirt a little silicone adhesive in the tubing and re-apply it.
This may not work for everyone, as I think there are a variety of other causes, but it sure turned the trick for me and I hope it will for you, too. Good luck!