1) poke around the rear rockers. it may look fine but sometimes it's already rusting underneath
2) check the trunk. pull the carpet to see if there's any rust - water may be leaking past the soft top/rain rail
3) look at the frame rails. they tend to rust/look fucked up - this is actually not really an issue but you can bring the price down a bit
4) alignment bolts. there are 8 of them on the car and on the last car I bought I broke off 5 out of 8 while trying to remove them. if you ever want to align your car, you need to replace all of them. $50. again, it's normal but if they look rusty you can argue etc etc
5) if the radiator plastic parts are brown, should be replaced
6) Check the gauge hood. Sometimes it looks fine but if you wiggle it around you may find out that all the tabs are broken
7) Rear finish panel is prone to cracking. Check it. It has no effect (mine has a 6" hole in it) but again, check it.