Diesel I'd do a Inter/after cooled 4BT Cummins and an NV4500. Depending on size of truck maybe even a B3.3 Cummins. I think I'd pick the OM617 from a MBZ before I'd do the B3.3 though, and there's at least one company that makes a reasonably priced adapter to put a Jeep AX-15 or NV3550 behind them.
For petrol power and economy, I've really been wanting to stick a GM S/C 3.8L (Grand Prix GTP, FWD SS cars and the like) into something RWD with a manual. I've seen a guy put the N/A version L36 into a '90s 4x4 Toyota Pickup, and is in the process of doing a similar swap on another one using the S/C L67 engine. He's pretty much got the junkyard adapter recipe to mate the Toyota 5 speed to these engines figured out. So the Dodge/Jeep transmissions shouldn't be that tough thanks to their similarities with the Yotas. I know of some rockrawler comp buggies with the L67 and TF904 trans. The 700R4 (or is it a 2004R) from the 2.8l S series trucks/SUVs and whatever manual they had should be "bolt on," since they're both GM "60° V6s" and whatever trans was behind the 3.4l V6s in the 4th gen F Bodies too.