This problem, and potentialy even the solution may not be new to some of you, but I have for some time now been frustrated by the door seals squeaking on my S3, it's quite common apparently not just on Audis but many other modern cars, but most can put up with it, ignore it or dont' even notice it.
It transpires that the problem is the door seals rubbing against painted metal doorshuts causes the squeaking, in much the same way as rubbing a dry finger on a well cleaned dry painted surface makes a squeak. The only solution to this problem is a lubricant. Now I tried a few products, and some are not to be recommended at all. Apparently silicon based products will degrade the rubber and you'll end up needing new door seals at some point, it also doesn't last very long, a week at best before a new application is required.
Eventually I was recommended the following product, and I can honestly say it's been a god send, it's called Krytox GPL105 (catchy eh?) and it's made by Dupont. It's a completely inert product so will not dissolve or react to water, car cleaning products, oil, grease etc etc. It's a very small bottle (30ml) but a little will go a long way and lasts far longer than any other product. VW re-package this stuff and sell it apparently for a lot more money, and in fact it's used by the wider VAG group for exactly the same application - although they never offered it to me as a solution!?
Application is a bit of a messy affair, it comes with a small sponge applicator but it's better to apply with your fingers and work it into the rubber seals, nooks and crannies. I applied this to the 2 doors and the boot door seal too. Word of warning, try not to get this on to the windows, plastic or seats as it is a real pain to remove, for the reasons given above.
It's not available in your average shop but I found the UK distributor who are very helpful and friendly indeed, GPR Limited whose details are:
GBR Technology Limited
Tel: +44 118 9820567
Fax: +44 118 9820590
The price for a 30ml bottle is about £41 inc postage. Quite expensive, but in terms of VfM, well worth it in my opinion.