There's good, better, best. Some of it really comes down to how you plan to use the bus. Quite a few engine and trans options in that category. First and foremost, can you drive a manual? Driving a stick is a skill that many seem to have abandoned in recent years, which usually means you can get a good deal on a manual-trans bus.
It also depends on the bus you're looking at. In the category you've mentioned, DT360, DT466(E) , T444(E), Navistar 6.9, 7.3, (basically a T444 with a few differences), 9.0, Cummins 5.9 / 8.3 and the Caterpillar 3208 are good choices that were offered in such buses.
The gas engines offered in the older models weren't bad, but be aware most are out of production and could prove difficult to get serviced. Avoid LPG / CNG / hybrids at all costs, unless you know someone who can convert an LPG / CNG engine over to gas or diesel, whichever applies.
A few came with Caterpillar C7s and 3126. Not terrible engines to my knowledge, but they were known to have electronics issues, and I've heard of the occasional head gasket problem as well.
Navistar builds a newer VT365 that Ford marketed as the 6.0 PowerStroke. Some claim Ford unintentionally sabotaged it, others say the engine is junk no matter what it's in. I personally would avoid them like the plague.
The Detroit 8.2 is a fickle beast. Okay engine, but has a wonky fuel setup that makes for a horrible exhaust smell and it is getting harder to find people who know how to service them.
I would stay away from Ford-chassis 2+ ton with hydraulic brakes. Problematic system with expensive parts and no one wants to touch them. Some Navistar buses may or may not have the same system. Some newer ones have an adaptation of this system, a hydraulic system with an air parking brake. Might not be a problem.
Avoid MaxxForce engines at all costs. I drove semis over-the-road a few years, and one carrier I drove just LOVED the International ProStar. I didn't, and neither did most of the drivers. Reason being that most of the MaxxForce engines stayed in the shop once they had some miles on them. I went through seven trucks in seven months, all had that engine.
Transmissions: Automatics are generally Allison, a good name, but not all are created equal. AT545 is what came in most. Basic, weak, and most need attention when they are auctioned off. The MT643 is better, the 2000 is better still, and the MD6030 is a gem. Some of the better ones can be tweaked to get better mileage and perform better through an Easter egg of sorts -- An extra gear hidden in the factory setup.
If you plan on highway cruising, especially mountains, I would skip the AT545-equipped buses, and try to get one with a bigger engine as well, such as the 8.3, DT466. The 5.9, some find to be a little underpowered on hills.
It pays to take your time and research the configuration of any potentials -- It's far easier and cheaper to find a bus better suited to your intended use than to try to make it what you wanted. Remember, these things are 12,000 lb bricks, most of which were built to haul schoolchildren at an average of 25-35 mph, not cruise the interstate at 75 and climb mountains. Also, for mountain driving (if intended) I would highly recommend air brakes and a basic CDL course ( you can learn a lot from your state's Commercial Driver's Manual).
Buses are available all over the country -- be careful when looking at one from the northern half of the country. Rust never sleeps and it has ruined more than one skoolie experience.
One tool that can help greatly in picking a gem or avoiding a headache -- FLUID ANALYSIS. Get samples of the engine oil, coolant, and transmission fluid. Independent analysis of these fluids can reveal whether the bus you're looking at is a good egg or a problem unit.
I would also highly recommend chatting up and befriending a good truck mechanic, they can be indispensable when looking one over. They'll know things to look for that you might not. There are a number of things that those of us here can think of to keep in mind that could happen, but it's best to bring someone who knows what they're looking at, for the reasons we can't think of.
Just my $0.02 (or $2.00, I guess)... Hope all that helps, happy hunting!