Who did your last oil change, and what oil was used?

It sounds stupid, but there is a special addative package for the TDI engines. Most synthetic oils do NOT meet the requirements.

Drain that oil unless it specifically says it meets the specifications for the VW ###.## that is listed in your manual. The pressure setup on the TDI's requires the extra additive package that the "unusual" VW spec provides.

It is possible its just the idler pulley bearing on your timing belt. Possible that it is the water pump, have you noticed coolant level being unstable?

That said, it could be something with the injectors finally starting to wear. If I remember correctly, the TDI uses injectors driven either by the crankshaft or camshaft, thus that special friction and pressure addative. I would highly suggest replacing that oil with one that meets the spec. In the event your car is under warranty, it is no longer as far as the engine goes. This is one of the few cases where what VW says is an actual thing that HAS to be done correctly.

I know http://www.gprparts.com/ carries the various special VW formulations. Check your manual as to which your TDI requires, as there are 2 or 3 very specific VW specifications out there for the various TDI's and other engines that have been manufactured.

I do not work for GPRPARTS, I just happen to be one of possible many customers. I am sure other businesses supply the same oil packages at similar prices.

Has the timing belt ever been changed?? If not that ticking could be a time bomb about to go off! Don't delay, change the belt if it has not been done. It was due at 80k mi. for 2002.

Was also thinking on this, as my wife's 99 Jetta has had this off and on.

Other then timing being off or needing a new timing belt...

I was thinking it could be one or more of the lifters not functioning correctly. If it doesn't pump up due to either wear/fault or lack of oil pressure, you would end up with just such a tapping noise as the cam slaps against it with less resistance and greater clearance.

I know this was the case before my 99 Kia Sephia was totalled after sitting for a week waiting on body work the first time. They ended up going in, cleaning and pressurizing the whole lube system and the lifters. Low and behold, no noise afterwards.

Nothing silly about double checking on a spouse's maintenance/or lack of

*Shuts up before he gets into trouble with his*

ok i have a99 beetle with 91000 miles i just went through this .my oil pump chain tensoner was cracked oil pump needed to be replaced .so while doing so i replaced timming belt and tensoner and had a valve job and oil pump chain tensoner .it runs like it did ten years ago when i bought it.im sure oil pump replacement will do dont wait cause you can cause a bigger problem if you put it off.good luck.