Well, most of the '98s and '99s have no problems with coil packs (unlike many of the newer 1.8Ts) so that's one thing to feel good about. As for areas to check, the control arms are probably the biggest thing. If they go bad, they'll cause squeaking and thunking in the front end, to my knowledge.
I think that is probably the biggest thing. If it's got more than 60k miles on it, make sure that the timing belt and tensioner have been replaced. Check that everything feels good when you test drive it. TRY EVERYTHING. Cupholders, vents, doors, hatch or trunk, folding seats, windows, locks, sunroof. If it's any sort of mechanism, make sure it works. Make sure that the gearshift, clutch, steering, and brakes feel normal, with no major hitches, clunks, thunks, snags, pops... if it feels kinda weird, then it's probably not right.
I say all of these things not because the Passat is known for lots of problems, but because anything can happen with a pre-owned car. I've got a broken vent in my '99... I've never heard of them going bad or breaking easily, so I'm assuming the previous owner (who also apparently tried to remove a dealer emblem with a screwdriver, judging by the scraped off sections of clearcoat) just smashed it somehow. Whenever buying used, remember: People do the stupidest things to cars. Run a CarFax on the car (you can probably find somebody who's got a subscription and can run one for you for free) to see if it's had any major problems.
With all of that said, I will offer my personal opinion to say that my Passat has been all but trouble-free, and I've certainly enjoyed driving it everyday. Good luck with your purchase! :thumbup: