I had a persistant musty smell from my vents whenever i turned the air con off. It was getting quite bad.
I checked the pollen filter and it was disgusting, full of crap and leaves. Got a new one from vw, only ?8. I removed the tray it sits in and hoovered up all the rubbish that collected above the plenum chamber (love that term) and put the new filter in. I also got some wynns airco cleaner and sprayed it into the system.
My car now smells lovely and fresh. I've heard loads of mk3 owners with air con complain of musty smells so i would recommend doing this to anyone. Takes half an hour and costs ?15.
By the way, i asked at the dealer about air conditioning cleaner, they said they won't sell the stuff to you, they will only take it in as a job and it would be 1 hour's labour and about ?20 for the spray!!!!!!