Dave, my friend, Jeeps... Are the One true 4x4.
I don't quite get what you're saying by "I can get a CJ without engine or transmission for this Cherokees, on the other hand, are much less expensive and are 4wd." Are you saying you can get a CJ7 without and engine and transmission for the same price as a XJ (Cherokee)? I find that hard to believe, so that's why I'm confused.
Also, I am almost positive that there were never any non 4x4 CJs made, except for the mail trucks. SOME XJs are two wheel only, but those are like the dirt cheap models. A little clarification here would help me out a bit.
On to your questions. " How are Cherokees in the reliability area? If I get a 6cyl, 5 speed with around 130k miles on it, is it likely to be on its last legs? What are typical problems with these, if any?"
This will depend on what year XJ you get. All XJs, to my knowledge, are fuel injected inline six motors. I don't recall off hand if the earlier models had the 258, or the 4.0 in them. I want to say that they're all 4.0 because they switched from the 258 to the 4.0 in the Wranglers somewhere around 94. Either motor is good for about 300K miles with regular oil changes. I'm not joking. Those motors are insanely rock solid torque monsters (well, as monster as you can get out of a 4.0 or 4.2).
As for the five speed? Who cares? There aren't very many moving parts in a manual. Clutch cylinder and the plate, that's about it. Sometimes the throw-out bearing will wear out before the clutch plate, but not very often. If the clutch plate hasn't been replaced at 130K, I'd be pretty impressed.
Things you will want to check at that milage: All front end parts. Brake calipers, u-joints on the axle, u-joints on the drive shafts, ball joints, steering arm, tie-rod ends, etc. Also, most of those are vacuum actuated 4x4. The front axles are always turning, but there's a collar that disconnects something inside the front differential I think, and the vacuum to the collar goes bad a lot, especially if it's not used. Some might be electronicly actuated, I'm not sure on that.
Bizkit is partially right. The automatic XJs have a fair number of problems with the trannies going out, and the xfer case is kind of weak so they like to die a lot if you're doing stupid things with them (like off-roading a lot, or pulling people out backwards, etc). For normal driving, you hardly ever hear of a burned xfer case. The trannies are weird though and often die. Again, if you're getting a manual, this isn't an issue.
Wranglers are rock solid nowdays, even with an automatic, but if you're looking at an XJ, I assume you want the cargo space. CJ, YJ, TJs are a little short on that.
Good luck in your hunting. Once you go Jeep, you never go back.