Take a good look around for rust. Check the rear wheel wells were they meet the body.
If you want your sami to have EVERYTHING it came with from the factory get familiar with what goes where. Lots of people ripped everything off in a quest for the ultimate 4x4 or just lazzy-ness.
Check or leaking oil/anti freeze.
Check 4 wheel drive
Check the diff's
Take it for a dive, nothing special with samurai's to check for compared to any other 4x4 whip.
For me the most important part was finding no rust. In fact when I bought mine it leaked oil in the engine, transmission, and transfer case; all of which I had to rebuild a few months down the road.
Ask yourself what is important to you and go from there.