I just came from having a mechanic check out a used 02 beetle and in addition to the above he:
disconnected hose from EGR valve and wiped out black crud with rag. He said this one wasn't bad, but that they can very quickly become clogged with baked-on crud. This is worse, he said, with non-synthetic oil, so it can help verify that proper oil was used. If caught early, cleaning it out can be enough, but in some cases the part must be replaced (at about $225 + install, I think he said).
Removed plastic cover over engine to inspect underneath.
Ran car with hood up (with and without AC) to listen to it.
Drove car on surface streets and freeway, checking performance and listening for odd sounds (such as from bad wheel bearing).
Checked under front of car for damage to plastic shield there (right next to intercooler, which he pointed out as a potential problem someday because the bug is so low). He recommended an aluminum replacement cover from
www.dieselgeek.com
Warned me (in Texas) against a black car because they get hot enough to damage some plastic and rubber components of lights, etc.
warned me about ease of breaking plastic (such as when replacing headlight) in cold weather.
Looked into crankcase from above with a flashlight. This one was very clean and thus it was a bonus bit of info, but I don't know how long before one should expect it to take befor it would look grimy there.
A lot of this applies to any car, of course, so maybe it doesn't fit the thread, but overall I was impressed that he really checked things out. After I'd spent two days really looking things over, I still learned a lot by watching him. Also saved me a little time getting oriented to the car (which wife is buying now) since he pointed out all the main parts and a few common pitfalls as we were going along. I felt lucky to be allowed in the shop with him while he was working.
Anyway, just my observations of his inspection. Take it with a grain of salt as I'm not an expert mechanic and I've never owned a VW before.
Keith