I had a problem recently with leaves and debris clogging up the drain holes (all of them!) on my 2000 GLX. I had the typical symptoms of fresh water in the rear and front footwells, on the rear passenger seat, and on my headliner. Found several excellent articles that described the location of all the drains, but had a hard time finding any actual images, so since I was going to tackle this problem anyways, I snapped a few pictures for posterity. From start to finish the project took about 20 minutes to clear all the drains.
LOCATION OF DRAINS:
New Beetles with sunroofs have 4 drains, two in the front on the driver and passenger side (very easy to spot with the sunroof open) and two in the rear (difficult to see without a flashlight).
WHERE REAR ONES DRAIN TO:
The rear drains (the easiest to service) exit near the roofline inside the rear hatch (see image). Each side terminates in a rubber nipple that often clogs with everything from debris to algae to mold.
HOW TO CLEAR REAR DRAINS:
Most clogs occur right at the nipple so "milking" it with your fingers usually clears the drain. If not you may want to try snaking a flexible piece of wire or plastic into it to clear it out better. I used a couple of stiff twist-ties hooked together to form a 2 foot long chain. It reached all the way to the drainholes in the sunroof.
WHERE THE FRONT ONES DRAIN TO:
The front drains go through the front pillars to a rubber nipple that you can not see just below the bottom corner of the windshield in the engine bay.
HOW TO CLEAR FRONT DRAINS:
The front drains are a bit tougher than the rear. If you have access to compressed air (not the canned stuff, it may not have enough pressure to blow out really tough debris like I had), you can try to fit the tip of the hose into the front drains and hope for the best. If this doesn't do it, you'll need to remove a few things to access the drain nipples.
You will need to remove your windshield wipers to get access to them. The wipers come off "fairly" easily. Pop the round plastic cap off the base with a flat head screwdriver, undo the retaining bolt, and wiggle-wiggle-wiggle the wiper arm off the splines (I cheated and used my socket wrench handle for leverage, but don't do that, it's easy to damage the plastic piece underneath them).