Ask me when I get my new-to-me 2006 NB I just bought for my wife sorted out.
This engine has good low end torque due to the long stroke, smoother than a 4 cyl so it doesn't need a balance shaft, has a couple of quirks as in known probably failure points, but no real bad warts, unless you think pulling the engine to do the timing chains is a really big deal.
So what are the known warts? The PCV tends to fail, the vacuum pump (yup, diesels aren't the only engines to have a separate vacuum pump, and its not even because of the turbocharging!!) leaks oil eventually, the evap purge solenoid likes to go on vacation, and the timing chains don't last forever.
PCV - this one has two, one integrated into the intake manifold, and one in the oil filter assembly. Figuring out which one is the problem is a bit of a challenge, but usually it is the easily accessible one in the intake manifold. The downside of that is that VW won't make it available separately, and you have to buy an assembly (not cheap). Or you can buy a Dorman replacement that might work for a while.
Vacuum pump - the seals leak so you'll get a small oil leak from it eventually. I don't think this one sounds terrible. Kind of tedious to get to it, or so I've read.
Evap purge solenoid. Also easily accessible, if it is the one I'm seeing, and supposedly they're not real expensive. I probably need one because the evap purge won't clear in the readiness codes. I haven't priced one yet. I'm going to see if I can clean the old one, but I'll probably buy a new one first.
The timing chains. Well, that one should be able to be postponed if there is an easy way to replace the tensioners without pulling the engine. VW doesn't seem to do these very well. Not sure anyone else does either. As it is, you'll need to consider doing something in the 120k mile range, but that is hear-say and should be independently verified by someone who really knows what they're talking about (read: not me).
Other than that, it seems to drive nicely, it starts, runs, and my wife likes the way it drives, more that it looks good because I suggested we put the gold painted fat fives with snow tires on for the winter shoes. The car is dark blue and looks good with gold wheels.
I would prefer a stick, but she won't have it. So...
Anyway, I like the quiet, smooth, and wife's positive vibes. The mileage isn't horrid; it should improve once I get the P2279/P0171 codes settled, and with the local price differential between diesel and RUG, there really isn't a big advantage mileage wise with a diesel over the winter anyway.
Our example has 80K plus a little miles on it, so the bigger problems are still a couple of years off.
That's my story, and I'm sticking to it.
Cheers,
PH