Technically speaking given the way a torque converter works the automatic guys actually can run their engines at lower rpms without lugging the engine-- where as you in a manual will have to down shift to increase your mechanical advantage. The real advantage comes when you decide to shift when accelerating or decelerating. That's when your manual gearbox really helps out because you'll shift at point when the car or truck feels better then with the automatic. As you you would be at the mercy of the automated system's programmed shift points. Sure most AT's use some form of simplistic adaptive system where they model their shifting behavior based on your throttle inputs-- that doesn't really help too much when do something like change the tires to a size 5 or 6 inches larger than stock. But on the converse the automatic works better at low rpm and gives you a torque boost.

It is also usually nice that manuals have closer ratio spreads and have more gears which helps to make up for things like changing tires or other modifications.

Personally, I prefer the manual gearbox.