Shoot at f/2.8. Check for center sharpness. Also, place three AA batteries in a row, approximately 2cm apart from each other. From about 45º off the line of the batteries (i.e. the batteries are not perpendicular to your image plane, but at an angle of 45º to your image plane), focus with your center focus point on the center battery and check for front/back focus. If the center battery is reasonably sharp, there should be little or no back/front focusing.
Shoot at f/4 and f/5.6. Check for alignment issues. By f/4 or f/5.6, decent corner sharpness should be attained. Shoot with subjects placed approx on the 1/3 and 2/3 marks, both portrait and landscape, and check that they are reasonably sharp. If one particular side is showing softness, it is probably due to misaligned elements.
By f/8 the image should be sharp across the frame. Check for alignment issues at f/8 again.
Otherwise, simple things like scratches and outer body appearance are minor things to look out for. Please don't be anal about dust inside the lens. A few specs is perfectly normal - no lens is dust free out of the factory.
