Number one on my list is to check the engine oil. Sometimes you can talk the seller into getting a free oil change and then check the oil carefully. Drain it into an absolutely 'clean' pan then slowly run off most of the contents into another container. With just a cup or so remaining, you should see any tell-tail signs of bearing material. It's gold in color and can be a few pieces or a large amount of fine bearing dust. Large quantities mean run from this deal as fast as you can.
Ride the bike if possible and check for any handling problems. Handlebars crooked, shimmy, shifting problems, engine noises, etc all spell problems.
A good way to check for rod bearing problems is to lock down on the front brake and with about 1500 to 2000 RPM load the system (don't let the bike move forward). You're listening for a knocking sound that should be far more noticable under load. Here again, if you hear a rattle or knocking, PASS.
Don't forget to check the gap between the tank and the inside fairings. The space should be relitively equal. If they're not the spill has probably bent the front fairing stay. This us easily damaged even in a fall off the side stand. Some of these are really expensive ($150 to as much as $400)
kanwisch's list covers most of the lesser items.
Don't let the small stuff scare you off. Just don't gloss over the really big dollar threats.
Be especially careful of customization stuff. Chrome wheels are usually ruined. Custom paint jobs are usually impossible to touch up. Avoid the wild custom junk, such as oversized rear wheel, Exrensive chrome plating is always a bad sign. I'd rather buy a bike with a bad motor than one fully chromed out.