If you haven't found your on personal lake in your car yet, consider yourself lucky. As our cars age, seals start to shrink and water finds more and more ways to sneek in. This bit of info covers the Scirocco, but can also be helpful in locating leaks in other VW's (or any car for that matter).
Look for dried mineral tracks left behind by evaporation, easy to spot against the black rubber. The short answer is to insert the silicon sealant (black) UNDER the lip of the gasket and run a bead all the way around, letting excess squeeze out. Do both gasket to body and gasket to glass circumferences. Don't skimp, a bubble or gap out of sight will fail the fix. The surplus can be removed before it sets up.
Inner Door Liner
The plastic liner between the door panel and the door shell redirects the water to the drain holes in the bottom edge of the door. Reseal or replace with any solid sheet of plastic. Bottom edge hangs down inside the door shell.
Quick solutions have been to recondition the things from underneath with black gaffers tape (almost like duct tape but not as 'tacky'). Pools of water will form on the passenger's side, where the fan intake is, if cracked or missing.
Rain Tray Drainage Tubes
In the engine compartment are two drain tubes to each side, near the wiper linkage, etc. Keep free of leaves and such to prevent backed up water flowing in the fresh air intake and into the dash.
Rear Hatch Seal
No great solution yet - still in development. Can be replaced with part 321 827 705A. Whole hatch area will be generally damp.
Rear Tailight Seals
Remove tailights and add a bead of silicon to the seals. Water will collect on the side of the hatch bottom.