Clearing the sunroof drains to avoid a wet interior or
fixing a broken line
difficulty: 1/5
Introduction
There are water drains at the corners of the sunroof that let water drain out to an exit at the door hinge. Twice a year, you should pour a cup of water down it to flush out any buildup that could block the drain. If it gets blocked, the water will back up and empty into the driver or passenger side footwell, causing possible water damage to electronics, mold, etc.. Regular cleaning will help prevent this.
Parking the car with the sunroof open under a tree can cause the drains to get clogged faster than normal because leaves, etc., fall into it. Mk3 passat sunroof drains exit into the fender. All other VW TDI drain into the door hinge area as pictured below.
Warning - if you do poke a hole into the line or it's already broken, instead of taking apart the interior, just feed a new line into the old line as pictured below.
Parts
weedwacker line or something stiff and flexible but not hard or sharp like a coat
hanger (too hard)
some water to flush out the drain
Cleaning Procedure
Open the sunroof and front doors. There are 4 drains at the sunroof,
one at each corner. A weedwacker line is pictured sticking in one of the
drains.

In the mk3 passat the drain outputs are in the
fender well and not visible. All other VW TDI have the drains in the door
hinge as shown by the weedwacker line.

Pour some water into the sunroof drain at the top and check for proper flow out the drain. This will also help clean out any small particles. I don't recommend compressed air because it might blow loose the line. If this happens, you have to remove the interior panels to repair the line. If it's okay, pour a lot of water in there to flush any particles out. If the line gets dislodged or you find water leaking into the interior, repair it using the steps below.
If it's not flowing well, use a weedwacker line to poke it clean little by little or twist the rubber exit drain with your fingers to open it. Do not use a coat hanger or anything that could puncture the drain line or else you will have to remove the interior panels to repair it, so don't force the weedwacker line!
Repairing a broken line
If you find that the line is broken, you must repair it to prevent electrical and interior damage. The normal procedure is to take the interior panel "A" pillar, the one by the windshield apart and replace the line. There may be an airbag in there, so disconnect the battery and follow all applicable cautions in your factory service manual if you have head curtain airbags.
An alternative is to put a new line inside the old line. Snake a hose into the sunroof drain and out the drain. Then trim to fit. If it doesn't want to go in through the top, snake the line in through the bottom. Pictures from volksbloggin.

Put a fitting in the end of the hose to prevent it from falling in any further. Use silicone sealant to hold the upper end in place and let dry. Broken sewer lines can be repaired a similar way instead of having to dig out the line.

Feel free to sign up and ask a question about this article at the forums here: myturbodiesel.com forums