*sigh*
A 2004-2006 is going to be a 100hp "PD" engine, that is going to require a rather expensive oil you may not be able to obtain from Walmart every 7000-10000 miles depending on your personal preferences.
All of these engines are subject to premature camshaft failure (especially the 2005.5-2006 New body Jetta MkV) if the wrong oil is used, and rapid failure seems imminent if a w30 oil is used in them for any period of time.
The repair cost for this assuming your oil pump doesn't go from the metal shardes of the shaft contaminating the oil is gonna be $3k or so... maybe less of it's a BEW code (non-5th generation) engine.
Avoid the Passat TDI at all costs. Just take my word on it.
What you WANT, if this is a commuter, and you don't care about it that much, and you're secure in your masculinity is a 2000-2003 Beetle TDI. It has 4 seat belts, so the resell is the lowest of all the TDIs. Manuals are easy to come by. It's got the same engine. 99-03 TDI engines are 90HP and bullet proof.
If you just can't stomach a beetle, a Jetta will do too. Tho, I have to say, ripping the back seat out of the Beetle I can put 2 55 gallon drums in the sucker. It's got a lot of room, and they're pretty cheap compared to the Golf and jetta (same chasis vehicle) with the 5th useless seatbelt.
The older engines (90hp) can use Rotella T6 oil, found at walmart and any truck stop. 10k oil changes no issue. The pump is the only concern, ironically, higher mileage means less likely the chance of a ring job for the pump -- 25k/year annual has been my baseline. I've owned 3 used TDIs now and I've yet to have a pump go on one, and see each one to 80-100k miles, the youngest of which had 114k on it when I got it.
There are a ton of modifications and performance upgrades you'll be inclined to make. Deleting the EGR and cleaning the intake being the first, removing the vent valve for the fuel tank so you get the extra 1.5ish gallons of diesel in the tank will be another. Chip tuning for performance, and large flow nozzles, another.
My personal experience has been 813 miles on 15.6 gallons of diesel fuel in a 1998 Beetle TDI. I left Byhalia Mississippi and drove to Ft Worth Texas and refueled just outside Little Rock Arkansas on my return. The car had no EGR, a cat and stock software. I never went above 65mph the whole trip...nor did I care to. Getting to my destination a whole 10 minutes sooner per hour really isn't that important to me, when I'm compensated for time and mileage as you are.
Let me also state that the 55-cent a mile federal reimbursement (or company reimbursement) works out to something like this:
2006 Jetta TDI. 33k miles in first year. 10,000 work miles. Avg price paid for Biodiesel 100% fuel: 3.50, Pump price: 2.86, I paid a 23% premium for my fuel for the year. 48mpg * 15 gallons = 720. 33000 miles / 700mi = 47 tanks. 47 * 15 = 705 gallons * 3.50 = $2467.5 for 33,000 miles.
10,000 miles at .55 a mile = $5500 reimbursement.
You do the math on what I made in the first year I operated my TDI for business.
Take my word for it, buy a 2003 or earlier. You'll see 50MPG readily on long trips, high 40s guaranteed.
Upkeep: Timing Belt every 100k miles $2000-$2500 or so having it done (not at a dealer, find an independant mechanic ... check our guru's thread), $350 DIY... we have a lot of GTGs where belt jobs are done for a good bargain if you can attend them. Having done the ALH and watched a BRM... the PDs are earlier to upkeep in this department, but either way the cost of the job isn't that bad.
Oil Changes: Top side, use a dipstick tube extractor (Pella 5000 is a recommended one) and it takes 4.4qt oil (5w40 full syn diesel oil; MOTUL or ELF are suggested for PDs and Rotella T6 for ALH cars) the filters are $10 to $18 depending on the vehicle. 10,000 mile interval (tho I did 7500 on my PD because of the camshaft concerns)
The fuel filter is $25 or so... you replace this as it plugs up, the book says every other oil change. That's up to you.
Suspension, bearings and other items like this will be anywhere from $300 to $1800 and depends on what you want to spend on it.
Brakes: $180 DIY from Autozone, $208 if you get the OEM stuff from a place like WorldPac, up to $650 to have it done professionally... again, your call.
Random bits I've had to replace: 98's Shift tower on the transmission broke on me. $215 to replace it in Memphis at Wolfsburged Automotive. I had the Fuel Shut Off Solenoid O-ring on my fuel pump also give out after the timing belt job 3 weeks later, $8 and installed it myself (diagnosed the issue on here, used a VAGCOM borrowed from a friend to test my theory). Interior panels, seats, and other stuff to personalize the car. I also had a camber issue and replaced the passenger front tire every 11 to 15,000 miles... I got 80k out of this car before I totaled it, it was so close to 280,000 miles... I'd hoped to see it hit 300k. Never rebuilt. These are SOLID motors.
Tires: No idea, that's a personal preference.
Misc: You'll replace power window switches, mirror control switches, a glovebox handle, possibly rebuild the driver or passenger door lock modules, the Brake Pedal Switch, possibly the cruise control cutoff switch for the clutch, and a few random little relays and such. All of this is well documented on this website, hint: go to google and type site:forums.tdiclub.com and then whatever your issue is and it will pop up a world of accurate results. DIY is your friend.
I just saved you a lot of research, so if you're over Carolina way (or Texas come Jan, I'll be driving there for a conference)... buy me a beer.
I've enjoyed these cars. I put a lot of miles on them, the 06 Jetta gave me 133k miles and I got it with 210 on the odometer new. I got rid of it because the camshaft was wearing out and I had already had to rig up the motor mount due to a manufacturing problem that took 80k miles to manifest. This is why I like old, used, you're already saving money with them cars as opposed to new bleeding-edge oh wow you're blazing a trail here buddy cars. I don't have the patience or time for it.
Your mileage WILL vary. Welcome to the club!