I was VERY close to pulling the trigger on a Jetta TDI so I'll forward what I have found:
1st, VWs are usually pretty good but there is like, 1 out of every 20 that JUST SUCKS. Nothing but problems and the other 19 are fine

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2nd, really haven't heard anything good about the 1.8T. I'd go with the stock 2.0 gasser or the diesel.
If you do go with the diesel, be prepared to deal with busted up cars with A LOT of miles on them, and then the god damn owner thinks it is made out of gold.
Oh, and around 100k, the diesels need their intake and some sort of valve cleaned. It won't cost you any money but it will require a day's worth of elbow grease.
3rd, the 1999-2003 jettas had problems with their headed seats. Heard stories of guys getting holes burnt in their britches. So check to see if they've been replaced (under warranty).
Around 120k, they start showing the normal car wear problems.
AVOID THE AUTO TRANS CARS. VW hasn't figured out automatic transmissions yet. I've heard nothing but terrible things about the auto trans.
Suspension is stout, so are brakes.
CVs go out around 120k. Apparently these are fairly easy to replace.
There are two trim levels: GL and GLS. GL = no arm rest and steel wheels with plastic covers. GLS = arm rest and alloy rims.
I've heard bad things about window regulators as well. I recommend you buy a trim piece tool and handle it.
VWs, like most German cars, they always want some sort of fancy oil. Keep an eye out for what has been in the car and keep using whatever it needs.
Fuel pump and filter...replace it. Fin. Do not argue this.
Lastly, it comes down to the previous owner. Like I said, I couldn't find a diesel that hadn't had the shit beaten out of it and the owner didn't want a crap ton of money. Some guy wanted me to pay $3k over KBB for a car with a salvage title

. I would say most 2.0 jettas were driven by girls so, be prepared for that.
The newer body style Jettas have REALLY come down in price. I saw a 2005 TDI with a 5 speed for like, $12k. Only had 60k on it. That is a deal. I'd rather pay an extra 4k for a car with 1/3 the miles and hadn't hadn't been destroyed. I looked at the non-diesel ones and they are sub $10k. The newer body style isn't as compact as the older body style but MAN they are nice.