Sunroof drain nipples as LNXGUY is the first thing to check since there is a known design defect. VW lost a class-action lawsuit over issues related to this. One source of trouble is the connection between the sunroof drain pan and the hoses (above the headliner). The other is that the nipples can get stuck closed. cut the end of them off or at least a nibble so water always can dribble out.
Also, are there any mods on the car such as aftermarket fuel pump? The instructions for installing that have a person drill a hole through an area next to the cabin air filter. If a person messes up that job it will leak there. Cabin air filter inlet could also be a source if there is something wrong with that assembly.
A/C condensate drainage is a potential source but since your issue corresponds with rain - not likely in your case.
Do you have damage on the headliners? Is it a new car to you or do you know all the history?
My car has had some leaks - an act of a higher power as far as I can figure out so far. It only leaks either during heavy torrential rain or during long sustained rain. Garden hose soaks and car wash did not cause a leak for me. Water appears on the rear or front floor - have not been able to trace the source.
for other reference, I have had the same trouble, ongoing thread linked below- maybe just me documenting to myself. I am still actively working on mine. Would appreciate it a ton if you update on any resolution of yours.
http://forums.tdiclub.com/showthread.php?t=419573