IMNSHO (since I own one), the best TDI to buy is an '03. It's the last year for the ALH engine and was towards the end of the Mk IV production run, so [in theory] most bugs had been worked out. Most cars were built in Mexico with the wagons (what I have) coming from Germany. That said, evidence the Mexican cars are inferior has been inconclusive at best.
Some other notes, mainly with regards to my own experience:
I have the upgraded Monsoon sound system. For a stock system, sound quality isn't bad (better than the Harmon-Kardon systems in our MINIs), but radio reception is crap and upgrades can be tedious if you want to maintain steering wheel functions. I would like to upgrade to a better system with MP3 and aux-input, but keep finding other things to spend my spare money on. The Vortex is better for this info than tdiclub.
Replacing the driver's headlight bulb will make you scream.
I've resisted the urge to do any sort of WVO conversion. For me, the amount of money saved is simply not worth the additional time required to do it properly and safely (for the engine). I'd be more interested in converting WVO into BioD, but again - time & space required. And then only because my home heating system could burn BioD as well, so additional cost-offsets can be had.
In all honesty, I tend to NOT recommend a TDI to most people. I have the space (house w/ garage), tools (lift, special service tools & VAG-COM) and back-up cars to service the TDI when needed w/o rushing anything. Because of this, the money saved on fuel isn't spent on keeping the car running. If you have to pay a TDI specialist to service the car, it may not pay.
Dealer service seems to be hit or miss. As mentioned, when I bought my car in '03, there were far more horror stories about dealer service than their were about dealer techs who knew what they were doing. It was this reason that I invested in the tools required to work on the car myself. My first TB change probably cost about $1000 in parts & tools. It will take at least 2 TB jobs for the tools to pay for themselves (although VAG-COM paid for itself much faster). With the increased popularity and acceptance of TDI's in the current line, I'd like to think the dealer techs are getting more/better training these days.
I would look for a TDI on the tdiclub forums. You may pay a little more, but it's more likely the car has been cared for.