All of the choices are pretty good. What are you looking for? Fuel economy? Torque?
I've owned a 2.5L I4/M5OD (manual), pushrod 4.0L V6/4R55E (4 speed a/t), and a 3.0L V6/5R44E (5 speed a/t). No major problems at all.
My '95 Explorer had the pushrod 4.0, 4R55E, ControlTrac 4WD with a Dana 35 front / 8.8" rear and 3.27 gears. It had the usual minor Ford issues at that age...clogged DPFE sensor, sicky IAC valve, but was bulletproof reliable. This engine burned NO oil with over 158K miles on it.
My '01 Ranger had the 2.5, M5OD manual, and 7.5" rear end with 3.73 gears. No problems to speak of. The check engine light never came on during the time I owned this truck, up to 93,000 miles. It got up to 28 MPG on the highway. The 2.3 Duratec is more powerful, just as reliable, and can get over 30 MPG on the highway.
My current truck, an '02 Ranger, has the 3.0 Vulcan, 5R44E, and a 7.5" rear end with 3.73 gears. Its one weak spot is the cam synchronizer. It's best to replace it as soon as it starts to make noise, and always use a Motorcraft replacement. Some engines never have this problem, but it's not unusual. I replaced the one in my truck at 60K miles. Right now it has 107K miles and runs like new.
I have never had a single drivetrain problem out of any of my trucks aside from a leaking xfer case output shaft seal on my Explorer (easy fix). The transmissions and axles have been completely trouble free with regular maintenance. The engines have been trouble free as well aside from cheap sensors and the cam synchronizer. I've never had an engine problem on a Ranger that wasn't fixed in 30 minutes. They are really solid vehicles.