I too have a 2000 Jetta GLS. It's a VR6, and has caused quite a few problems even though I baby it all over the place.
Both front window regulators have been replaced (One at 15K miles, the other at 20K miles) when the car was under warranty. Now the front passenger doesn't work again. Was opened about 4 times before it broke the second time. At $200 to get it fixed, it can just stay broke.
The oil pan has aluminum threads and is "Designed" to fail after a few oil changes as the steel drain plug strips the aluminum threads if tightened enough. Dealer advised me that torquing the bolt to the recommended 35 pounds wouldn't be tight enough and would risk plug coming out at any given time. Solution was to get a steel sleeve placed into the oil pan for the drain plug to fit in. $75.
Mass airflow sensor failed at 35K miles, cost $400 to diagnose and fix. Got damaged "because snow screen was dirty". I only drive paved roads in Pittsburgh, so there is no reason for the snowscreen to be dirty. To this point have had all scheduled services done at dealership, so no reason for this to happen.
Both slats in the rear window between the window and quarter window have rusted (One at 20K miles, the other at 30K miles). Dealership has to remove the window to replace a 2 inch strip of window. Had one replaced under warranty. The other one can rust through at the cost of 2 hours of labor.
CD changer decides some days to skip on all tracks on all cds. Has done this since about 10K miles.
Costs $165 to get the spark plugs changed, which foul and need replaced every 40K miles, when other makes can go 100K miles between changes (!!)
Rear brake pads needed replaced at 30K miles. $160. Rear brake pads shouldn't fail before fronts. Dealer charged $90 for pads - which can be purchased from a supplier online for $27. Apparently, it is common practice to mark-up parts 200% to 300% and still overcharge for labor.
Owners manual is terribly skewed toward leading you into ignorance. Doesn't even tell what to torque the drain plug to. (other makes tell you much more technical information than this). After most problems, says "take to dealership immediately"
When bulbs burnt, dealership wanted to charge a half hour labor to change each (?!?!) as well as 300% mark up on bulbs. Went to Wal-Mart and purchased the bulbs an installed in about 2 minutes each at cost of $3 per bulb.
Service department is closed on Saturdays at dealership.
Oil filter is only the filter element, and costs about 4-6x as much as a regular oil filter for no reasn and with no benefit. Costs more just to purchase a filter than it does to change oil and filter in most cars.
Car demands 91+ octane fuel for a rather low performance engine.
If you fill the oil to the top of the indicator on the dipstick, and then park on a downhill, the engine will burn oil off and ruin the catalytic converter.
DO NOT BUY one of these. They're probably the worst of the cars in their class as far as failures and cost of operation.