I had same problem on my A3 since day one. Here in Italy this problem is very usual due to poor roads everywhere. The noise comes from upper door seal (the one having double lips) especially when the contact between seal and body is not perfect (see below). Yes, sometimes our expensive cars are far to be perfect ...
I tried all kinds of liquid/cream etc, from cheaper to most expensive ones (i.e. Tunap at 30$ ...). Audi Service itself applied some specific liquid which didn't solve the problem. The only solution which works great - I mean that you need just 2-3 treatments per year - is a silicone cream for leather which is cheap enough, is transparent, has a good flavour and doesn't leave unpleasant traces. I'm talking about this one:
http://tinyurl.com/js6fszb
It's really great ! Just apply it with a small brush along the entire seal then remove the surplus, and then apply it again. This way you will get rid of this annoying problem DEFINITIVELY.
But ... you will just kill one of the effects, not the cause (another effect is the extreme wind blow from side window which unfortunely will still remain...). The "original sin" is the
misalignment between the door and the body frame. I'm talking about the alignment with respect to the CENTER OF VEHICLE which can weaken the seal grip. In my case, there was a gap of about 2-3 millimetres between the upper and lower side of the door. In practice, the upper door contour stuck out more than the bottom which instead had been assembled slightly inwards (2-3 mm).
These few millimetres can seem negligible at a first glance but they are VERY IMPORTANT. A quick visit to my body repair Service and ... no more rattles, no more wind noises !
My best regards.
David from Rome (Italy)