The list is endless. But remember the engine compartment was not designed with length in mind. So rule out most all straight diesels unless you want to make a small doghouse in the cab. There are a multitude of good gas V6's and gas/diesel V8's that will all fit very easily. It ALL depends on what YOU want.
You wanted insight on clearance issues and common hurdles involved in GMC engine/tranny swaps. Here they are. Yes, this is all of them.
-Clearance is usually a non issue. SOME oil pans may hit the differential. SOME exhaust manifolds (right hand) will hit the large cast iron casting on the right side of the frame that connects the torque rod to the top of the front axle. It can be trimmed but the usual procedure is to cut the manifold short and weld on a 90 degree downpipe.
-Brakes. You will need to fabricate a new mount to remount the GMC air compressor. It's the cheapest option and by no means a bad one. Lots of advantages to on board air. It's the simplest option, the air compressor can be plumbed into virtually any engine you can think of for the oil/coolant. Just a matter of fittings and hydraulic hoses from NAPA.
-When you ditch the Hydramatic, you have lost low range. If your an asphalt queen, it's no biggie. High range is still low enough to move 10,000lbs on level asphalt. Forget offroading with a load. If you want low range back the easiest option is to use a 2nd Tcase to drive the STOCK GMC Tcase. It's "special" to the GMC series as it drives the front axle shaft backwards. Part of the design.
-With the Hydramatic now gone, so is the original shift linkage and shift tower. The original shifter did two things. One, it shifted the Tranny into the selected gear, but it also simultaneously shifted the Tcase into forward or reverse. It basically had to tell the front sprag inside the Tcase which way to turn so it wouldn't bind. I had no need for front wheel capabilities so instead of fabricating new linkage/levers to manually shift the Tcase, I just dropped the front prop shaft, drained the axle housing and pulled the shafts. So the front is free wheeling. Also eliminates the chances of gear oil leaking into your knuckles.
Not recommended if you plan to drive in snow, mud or do offroading.
Oh. And make sure you have the tools to cut and weld 3/16" steel regularly. If you can't weld you'd better start quick.
Let me know if you need anymore info and i'd be glad to help.