I know a guy with a TDI Jetta. He's had a few electrical problems, but nothing major. I think it's an '02, but I'm not sure. Manual transmission, 50mpg is pretty common. He can do about 700 miles on a single fillup. I think the electrical problems are a VW problem across the board, not specific to certain models. I heard at one time that certain special edition models (ie: Wolfsburg edition, etc) had fewer problems, but I have no idea if that's true or not.
The number one complaint I have about the Jetta is the non-exsistant back seat. There's hardly any legroom.
It might seem like diesel fuel is a lot more expensive, but that's not always the case. Around here, the price of gasoline dropped way down ($2.15), but diesel hasn't really dropped (~$2.80). According to Edmunds, manual transmission gasser gets 31mpg at best. The TDI is 49. Both have a 14.5 gallon tank.
Assuming a full fillup, the gasser gets you 449.5 miles for $31.18, or 6.9 cents per mle. The TDI goes $710.5 miles for $41.33, or 5.8 cents per mile.
If I were looking at two VW Jettas, both the same price, but one was a TDI and the other was a gasser, I'd go TDI every time. Of course, good luck getting a TDI for the price of a gasser, the word is out on the mileage and their resale value has gone up accordingly.
Edit: OP, TDI club may be a good place to check out.
http://www.tdiclub.com/