One thing to look for is cracks in the frame. In particular, look at the bottom side of the frame around where the head tube is welded. Bikes that have been wheelied to hell and back tend to crack here. Most people dont usualy take the time to contort around to look for crackes in this area.
If you are looking at newer sportbikes, walk away from any bike that has bent forks. If the forks are bent, chances are that the frame is tweaked too.
Also, look for mis fitting body work. If the body doesnt seem to hang on the bike properly, there could be problems.