The motor configuration was hard to keep tuned and reliable. The base motor is good enough, but the supply setup is terrible. Also, they had terrible trannys prior to '91 that were prone to breaking and cost a lot to get fixed. YJ's are nice jeeps, but I wouldn't settle for one prior to '91.
As to the CJ's, There were CJ-5's (until 1983) which had an 83" wheelbase. They came with a variety of motors and drivetrains, some of which I would stay away from (SR-4 transmission). They were nice off-road but the short wheebase tends to kick them around on the road a lot, making for a harsh ride.
The CJ-7's were produced from '76 to '86, also in a variety of configurations. They have a 93 inch wheelbase and are nicer on the road. More parts are also more readily available for them (tops, doors, etc, new and used), IMHO, but the used the same drivetrain and motors. They are a little easier to lift due to the extra length of the wheelbase, which makes the driveline angles less steep.
There were also CJ-8's, or Scramblers, which are a little rare. They have a 103" wheebase and were basically a lenghtened CJ-7 in the form of a pickup. They were produced from '81 to '85 and came with the half cab (pickup) and the full top. They also had the typical jeep drivetrain of the era.
As to which one to get, I'd personally look for a CJ-7 (or CJ-8 if you can find one) or newer Wrangler. Look for one with a 6cyl motor (straight 6), the 4 cyls tend to be a little underpowered. Also, avoid the SR-4 transmission of the early '80's CJ era, they're junk and won't last. The 1986 CJ-7 had the strongest rear axle, but the others will hold up well. My personal preference is the earlier ('82 to '78) CJ's as they had no emissions crap on them, easier to work on and less restriction on the motor.
As to what to look for, check out the rear frame for rust, behind the rear wheels and on the inside. If the frame is going to rust, it starts there first. Avoid something that has been heavily modified, you never know if the person did a good job or a hack job. Unless you have tools and place to work (sounds like you're looking for one to drive), look for one in decent condition with little wrong with it, don't settle for "Well, it only needs..."
Most people tend to modify their drivetrain, putting new motors, transmissions, axles and such, but the stock jeep is a decent vehicle. We modify them to match our needs and wants. My Scrambler is somewhat modified, but it sees very little street use, it has terrible road manners and beats me to death when I drive it. Off road is what I built it for, I have other vehicles to drive on the road. A lot of us also have tons of spare parts lying around due to all these mods, so if you find a jeep that needs something, ask or check out the Wanted Board, you might find it. Good luck in your jeep search, I love looking at jeeps but the wife cut me off after our 5th.
JEEPN
'81 CJ-8 Scrambled!
GM151/SM465/NP205 twinstick/7"Lift/33"TSL's/IHC D44's 4.10's Lock'd
