Being someone who owned a 2003 Golf TDI, I used to frequent the tdiclub forum, and read a fair bit about the new TDI engine. While all of the "clean diesel" related gadgetry is new (and therefore doesn't have a long track record), the engine design itself was apparently an old proven one, used in other markets for quite some time. This TDI engine is a common rail design. The North American "pumpe duse" engine used from 2004 to 2006 was a bad design in my opinion and one to avoid, but this engine is completely unrelated to it.
Electrical issues seem to be a continuing VW (heck, any German make) problem, though the unit I had didn't have any issue in that department, other than bulbs seemed to burn out more frequently than other cars I've had.
Transmission wise, stick to the manual. VW seems to have good manual transmissions. In '03 and older, they had a horribly unreliable 4 speed automatic. That was later replaced by a 5 speed automatic (not sure how reliable that was, but certainly better than the older 4 speed). They have since moved away from conventional automatics to the "DSG" design (an automatic manual for lack of a better term), however it's a new design, and there have been some issues with it relating back to the design itself. A little known thing about these is at idle in traffic, you need to slip it into neutral, or you will get accelerated clutch wear.
You should be quite happy if you take an active part in the care and feeding of your cars with a manual model. Do lots of homework and know what you're in for if you decide on a DSG.
