I went through this with my Jeep. There are choices out there, but a lot of them stink. The ones I can think of off of the top of my head:
Nissan/Scout SD33 -
Outdated. Underpowered. Not much parts availability. Can be had with a 727, but it makes it even sluggy-er. Turbos were there mainly to clean up emissions, not to make more power. They are all slow.
VW 1.6/1.9 -
ACME has cheap adapters. I believe you can use a Toyota or, actually, a Volvo automatic. The 1.6 is way underpowered as well, but it could work if you keep it 2wd and the motor was in good shape. The 1.9 makes a bunch more power, but you have to deal with the electronics or convert it to manual injection for more $$$. Decent parts availability.
Mercedes OM 4 or 5 cyl -
Some of them are on the weak side, some of the turbo 5 cyls are actually pretty decent. Odd front sump that can be a pain to work around. 4x4labs has an adapter to run a GM manual transmission, stands to reason an automatic would work as well. The mercedes automatic is not bad either. There are a bunch of these cars still on the road and parts are around.
Detroit -
You will be dealing with the 4 cyl or less motors, even a 4-53 will come close to crushing the front of your Jeep. I have seen some 3-53 and 2-71 conversions that look pretty cool, but you need to know a lot about detroits, good mechanics that understand the old detroits just are not around as much any more. There were some automotive bellhousing adapters out there for a transmission. I would avoid them unless you know what you are doing. Parts are drying up as well.
VW-Motori -
Run.
Isuzu -
The 4BD1t is a good motor, somewhere between the 4BT and the 4A power wise. Good parts availability. Good transmissions, and adapters out there to go to the GM style transmissions. Lots of them out there in delivery trucks, parts are easy to find.
Mitsubitst-Fuso -
They have some 4 cyls like the Isuzu 4bd1t, but parts are just not here. Good if they are running, but last I checked rebuilds are 2.5k for just the parts. Like the SD33, just not a base for them in this country.
Cummins -
4a -
Good little motor, phoenix castings makes a good SAE4 adapter, parts availability is good from Cummins, but can be sketchy from anyone else. They were never put in road vehicles, so you are on your own with an accessory drive, unlike all the rest of the motors listed. They have an alternator, but AC, power steering, etc. is going to have to be fabricated.
4BT -
I am a little biased because this is the motor I want with, but I think it has some really good things going for it:
My accessory drive is from a 89 Dodge Cummins truck. Parts are easy to find.
It makes good power, and it is easy to turn up if you want more. Most of the modifications are well proven from the big brother, the 6BT.
My adapter is a factory Dodge adapter, so flywheel, starter, etc. is all very available.
For my application, the 4BT was an easy somewhat bolt in swap with good parts availability, which is what I was looking for. With some more creative work any of those motors would work just fine.
Besides, a 4BT looks great in a Jeep engine bay!