Here's a checklist I have compiled of stuff that you can easily check at the dealer while looking at the car or during a test drive.
-Check the panel alignment. With these cars, it's not too hard to tell when they've been wrecked. Often times, the headlights not aligning properly with the fenders/hood/bumper is a dead giveaway of front end damage.
-Check for original glass. It will have Audi rings in the corner if it is original. Non-factory glass could be from a simple rock chip or from a significant accident.
-Check the stock wheels if you plan on keeping them. Usually the six spokes are in HORRIBLE condition. I was fortunate enough to have the dealer completely refinish mine.
-Mirrors are both powered and should be heated at all times. If they're not, something's busted!
-Make sure the seat adjustments work. Check knob on the side for the backrest and the lever on the side for the up/down motion. Make sure the seat heaters work. Not sure how much these cost to fix.
-Rips in the leather will only get worse. If the car's well taken care of it shouldn't be ripped. OEM seats run $500 or so for a used set of fronts.
-Make sure the glovebox latch works...smoothly. Glovebox is $300-$400 on eBay, $700 new from dealer.
-Make sure the headlamp washers work and don't leak. Mine had a dead fuse. When I discovered them after replacing the fuse, I also discovered they leaked. From then on I had persistent washer fluid warning lights until I finally found the leak.
-The surface of radio buttons on some of the newer radios are often worn out. The black buttons will be worn white...you can insist the dealer fixes this or use it as a leverage point for negotiation.
-The dome light is intermittent because of poor wiring. It generally doesn't die however, so if it doesn't work, it probably just needs a good punch. Don't be alarmed.
-Check the instrument cluster. Make sure the lines on the display aren't dying and that none of the gauges read erratically. The speaker in it can die too. Cluster repairs are $1000+ at the dealer. There's a class action lawsuit for repairing them, but it doesn't apply to older cars and expires very soon I believe. A cluster can be had for around $200 second hand, however it has to be checked for compatibility before hand and programmed by a dealer or someone with VAGDASH-COM* See my cluster info post.
-Make sure the turn signals work properly. The relay is $50 to replace. The stalk, which can also fail, is over $100 to replace if I recall.
-Check if there's a CD changer magazine. If there isn't, make the dealer order one. It's $30 and annoying to be without.
-Check if it has the rear hatch cover (coupe only). It's another small, annoying piece to not have.
-Make sure the windows work. The switches for them are behind the handles.
-Make sure the windows both roll down/up SLIGHTLY when you open and close the doors. This is a standard feature to keep them from shattering. If it doesn't happen, something could be broken (with my car, a wiring harness was to blame).
-Check for leaks if you have a chance. First time I washed my car the hatch leaked. Prompt trip to dealer and it was fixed.
-If it grinds while going into second, this is a normal synchro grind. It's unpleasant, but it happens.
-Creaking from the front end is the front swaybar bushings. $50 for a poly set, I believe it's around $14 for an OEM set.
-Power should hit hard around 3000RPM. If it's delaying more than that, there's something wrong.
-The car revs quite high. At highway speed, it will be between 3000-35000 RPM on the five speed tranny depending on how fast you're going.
That's all I can think of. Send me stuff to add if you think of it.