Have a look in the boot, under the carpet, in the spare wheel well. I've had my GTI for only a few weeks, and I've got the same problem with condensation. I've discovered that water is getting in through the boot somehow (I can see it trickling down the panel that clips into the body of the car at the back, directly beneath you when you lean in the boot) and it slowly fills up in the spare wheel well. If we ever get a dry day again (!) then I'm going to take all the trim out and try sealing the leak, provided I can find it.
I've read a load of threads both on here and on VW Vortex that suggest the rear cabin vents (located behind the trim panels and below the rear light clusters) are prone to leaking - the seals don't seem to have been particularly well made and it's a pretty common problem on the Mk4. You need to take the bumper off if you do discover it's these that are leaking and you can then seal around the edges of them with bathroom sealant - I think I'm right in saying that, but you might want somebody else to confirm.
I've got no problems in any of the footwells, so the water isn't getting in through the front of the vehicle, but I get a nice little paddling pool under my spare wheel. It'll be good on a hot day
