From JeepTech and JeepTech Publishing LLC, the Jeep knowledge base.
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The first thing to consider when doing an engine swap is it will cost you three times what you expect it to cost you. If you are going to take on a project of this sort, you need basic wrenching skills, some fabrications skills, and an understanding of how things work.
Swaps are generally cheaper and easier if you match the transmission with the engine. If you plan to swap the transmission as well, do it at the same time and get an engine and transmission that will work together easily. Many Jeeps used Ford pattern transmissions, many use GM pattern transmissions. The swap will be easier and cheaper if you put a 302 in a '78 CJ over a 305 for instance.
I get a lot of email from people with Jeeps with I4 engines that want to swap in an I6 engine. Don't even bother, it will be far cheaper to sell your Jeep and buy one with the engine you want.
Chevy V8: Putting a Chevy 350 or 305 in your Jeep can be a great swap for almost any Jeep. It has been done before, parts are fairly inexpensive, and there is great aftermarket support.
Ford V8: The Ford 302 and 351 make a great swap in most AMC era and later Jeeps because many of these Jeeps used Ford pattern transmissions.
Buick V6: The Buick V6 225, 231, and 252 are great swaps for most early Jeeps because of their external size, power, and cost.
Chevy V6: The 4.3L Chevy V6 is a great swap for nearly any Jeep. They all come fuel injected and the early versions had an extremely easy to understand and diagnose TBI fuel injection.
Chevy V6: The 3.1L and 3.4L Chevy V6 rear wheel drive engines are a great swap for 2.8L equipped MJ and XJs. The 2.8L is also a 60* Chevy block and the 3.1/3.4L will bolt in with only minor mods. The newer Chevy designs are a great improvement over the 2.8L. The owner can stick with carburetion and just swap over everything from their current block or try their hand at wiring in the 3.1/3.4 MPI fuel injection. 3.1/3.4L engines are generally found in late 80s and early 90s Camaros and Firebirds. Front wheel drive engines will not work.