There's going to be a guy who shows up in here and posts his reasons why people who say "buy a 99" are lazy.
Yep, because I think that your answer is lazy. "94 or 99?" Really? Back that up. Tell me why not 95 or 96 or 98 for instance? I'll grant you that 94 was a little more sturdy than previous years. You probably don't like 95 because...what?...it has an airbag? That's the only significant change from 94-95 I can think of. An airbag rules 95 OUT for you? Most people consider that a plus. You another one that rules 96 out because it's a "transition year?" I owned a 96. There was nothing transitional or mysterious about it; it was made in Sept 95 (you can know this simply by looking its VIN up through Jeep or even a Carfax service), so maybe the later ones were a bit mixy-matchy, fine. What's wrong with 98? No 99 intake? So what? After years of periodically researching and re-researching the topic, I've seen proof of NOTHING regarding the 99 intake other than it gets in the way of fitting the APN header. Lots of speculation, but never any actual proof.
I'll accept not wanting to call pre-91, 00/01, or even 97 (hard to find accurate wiring diagrams) the "best," but nit-picking further than that starts to get a bit absurd.
Guys whose only advice to you is "buy a 99" aren't really helping you much. Some of them just blindly regurgitate that because they read it somewhere when researching Jeeps, and they don't even know why. There are some reasons that 99 is a particularly favored year, but it might be that NONE of them matter to YOU. I mean, what do you want to do with your Cherokee? Is it just going to be a daily driver? Will you wheel it? If so, how often? How hard? What kind (mud, sand, rocks)? Are there any particular modifications/upgrades you'd want to do to it?
I think some people's obsession with 99 is a bit disrespectful to how great all the other XJ's are. Even the 00 and 01 XJ's are worthy of respect that is often denied to them by many. You really can't lose. Many minor and some major changes were made between 84 and 01. I'm sure you can find a list of all the changes out there somewhere; I know I found that info myself once upon a time.
Aside from the normal stuff to look out for with ANY used car, be aware that 84-86 XJ's had GM engines that pale in comparison to the 4.0 of 87-01 (I'm just ignoring the 4 cyl engines that some XJ's had). The pre-91 Renix systems are a bit ... "special" and simply something to be aware of and ready to work with if you're looking at one. 00-01 4.0's have a head with a casting flaw that may or may not crack between cyl 3 and 4. Many of them never crack (or at least haven't after hundreds of thousands of miles), but many do. It's something to watch-out for but not something that should keep you away completely, and you should be aware that identical heads without the casting flaw are out there should you have a crack. The manual trannies are solid as are the autos. The two possible transfer cases are both great. There are a variety of rear ends each with their own advantages and disadvantages, and unless you're planning on doing lots of wheeling, even the weakest of the bunch (D35) will be just peachy. The floor pans are easily the most susceptible to rust on all years. Because of the limited space for a radiator, XJ's are just barely able to maintain their operating temperature, so you have very little room to slack on maintaining the cooling system; luckily the cooling system is a reliable as any other part of the 4.0, so it's not likely to require much work (and any work will be relatively cheap). The stock exhaust manifold cracks easily which can impact the performance and efficiency of your engine negatively. APN makes a replacement header that is a very affordable replacement should you ever need/want one (there are other header options out there as well).
It is my opinion that if you get an XJ with a 4.0 from 91-99, you have virtually nothing but cheap regular maintenance to worry about. If you get an 00 or 01, you just have to make sure to never overheat it (as if you'd ever be OK with overheating any engine), and to pay closer attention to the oil and coolant "health."
OP, if you want to learn about some of the more insignificant changes throughout the years, look here: http://www.edmunds.com/jeep/cherokee/history.html
Price is very variable with geography, and common problems you may see immediately are header crack, rust, overall neglect from ignorant previous owners, rust, and oil leak from oil filter adapter. And rust.
Autos and manuals: neither is better. They'll both survive the apocalypse. Manuals will get you better MPG, but autos have the simplicity/ease of being an auto. It's just up to you (or fate since you can only buy what you find).
I will say that you should make sure that an XJ is big enough for what you need before you buy one. 2 people, 2 dogs, and gear...might get a bit cramped in an XJ depending on the people/dogs/gear. ZJ's are a bit bigger, and WJ's are even bigger. Yeah, I know the looks are dramatically different, but the guts are all basically the same especially if they all have the 4.0 (ZJ's 5.2/5.9 V8 is also quite great, but I'm not a fan of the WJ's 4.7 V8 at all). Just food for thought.