Currently I have two 2006 jetta tdi vehicles. One just passed 30,000 miles; the other has about 1,000 miles. Both have the DSG (auto) transmission. Other VW diesels I've owned include an 85, 92, 99 (pretty sure that was the year. Wife's car, so I didn't pay much attention) and 2002. the 85, 92 and 99 were al sold after they past about 150,000 miles. They were all running strong and looked good. I traded the '02 on the '06. I got a couple of weeks ago. It only had 80,000 miles and I should have kept it. But, it was going to need tires, timing belt service, and brakes (sometime before 100k). I'd feel like replacing the struts when I did the brakes. So, instead of spending the money I sat down with the local dealer and got a pretty good deal on the 06 and decided to do it. That way, I'd have a fresh jetta in the stable when I'm ready to sell the forester and get a diesel Tourag if the come in with a smaller engine.
Everyone has different experiences, but the only thing I've done to my VWs is change the oil & filters and other routine maintenance. My three porsches were about as reliable as the VWs, but they did require more servicing. Can't say that for the mercedes vehicles I've owned or the U. S. brands. Never had a japanese car--just don't like the road feel. Come to think of it, I did replace the alternator in the 85 at about 140,000 miles.
You can do a lot of the work youself if you have the tools, the time and the interest. The TDI club site you seem to have found has some great information and their are other resources. I use to do a lot of my own work, but I just don't have the time anymore.