dmax, short drives do not cause as much of a problem as you insinuate. Maybe repeatedly starting and moving the car 1 block, but it's not going to kill a battery. And yes, flyback diodes in the alternator. It is just good practice to turn the car off after the donor car's alternator has charged the dead battery up. You generally don't have to rev it up, either...most alternators will deliver enough current at idle. On an older car, it might be worth trying.
I would leave them connected for at least 10 minutes if the engine isn't cranking at all. However, if you're not getting anything after that time, I stand by post #2. You should at a minimum get a "wuh-wuh-wuh" even if the starter spins the engine too slowly because of low voltage.
Under hood or at the battery should not matter--the cables in the car deliver power to start, so obviously they're adequate to deliver current from a live charging system to a dead battery. Still, at the battery is better.