2003 Jetta TDI wagon GLS 5 spd. Purchased new; ordered to spec. currently with 329K miles. Original clutch. I've done maintenance to it, but that's pretty much it. All work DIY.
Issues have been few:
Sunroof developed a mind of its own and would open/close by itself. I never use the sunroof (part of the GLS package that was required if I wanted leather) so my solution was to pull the fuse.
I got a bunch of CEL related to the glow plugs, and I replaced them twice. I replaced the wiring harness at 200K and that seems to have fixed it.
One MAF sensor at ~140K miles. Went into limp mode and smoked like an old truck. No CEL. Pulled the harness plug (that gave a CEL), which puts the ECU into a 'default' setting and it'll pretty much drive normally until a new MAF can be had.
They're prone to coking up the intake manifold and EGR valve. I pretty much swap the manifold as a maintenance item every few years (have #3 waiting to go on). It's amazing the engine will still run with the manifold 75% clogged. Other solutions are to delete the EGR (requires an aftermarket tune), turn off the EGR via VAG-COM/VCDS, and put a oil separator into the PCV line. The latter doesn't solve the initial EGR coking and the former options tend to reduce fuel milage.
I received notices for three recalls: the break light switch, the sunroof drains, and the seat heaters. The break light switch I bought for $5 and replaced myself (less hassle than havign the dealer do it for free), a GRM member sent me the bulletin to fix the sunroof drains, and I ignored the seat heater recall since I'm 99% sure the 'fix' is to swap the switch out to one that will reduce the power to the heaters and I didn't want that (the seat heaters can cook you!).
I added an aftermarket coolant heater to plug in during the winter. The car still starts fine in sub-zero temps, but it's just a lot happier if it's been pre-heated a bit. Especially if I can't put it in the garage.
Now I'll admit I haven't driven the car since November. The inspection expired 2 years ago, and I suspect the turbo is about done, so I was collecting parts to replace everything. I finally got it into the garage last w/e, but I stuffed the mother's Volvo into the garage as well until the pending snow is passed.
I agree about manual HVAC controls. I like having 3 simple knobs that will do exactly what I tell it do when I tell it to do it. I have a rather intense hatred of the Auto HVAC system in the MINIs. The A/C in my wagon works very well and has no trouble cooling the car even on 100+ high-humidity days. The heat works well too after the engien finally warms up (although the TDi warms up faster than the damn 3.3L V6 in my Caravan).