Really, most of the stuff is cheap and easily replaceable.. especially if you aren't trying to find a working unit.
That being said,
Parts removed from components you think are working (some of my coin doors have been missing parts)
Insects.
Water damage in odd places.
Cabinets that aren't structurally sound, or have visible screws in the outside of the cab.
Missing back panels
If you want to use the controls that come with, make sure the joys are the type you are looking for, 8 vs 4 way, leav vs. microswitch. Same with the buttons. I have cabinets with mixed microswitch vs leaf buttons.
The way the control panel attaches. Is it metal or wood. If you want to mod the existing control panel, most people find the metal ones more difficult to modify. (I say, just build a new one anyway)
I try to make sure the monitor is installed in the machine, so I can swap the mounting brackets on a TV. I like using TVs, and finding mounting brackets is tough.
When I buy a cabinet, I try to get a cool looking cabinet, and I don't worry about the components AT ALL. I just make sure the cabinet isn't going to fall apart when I put it in my van. I bought a machine that did almost fall apart when I put it in my van, once. I would do it again, though. It turned out to be a really fantastic cab when I restored it.