DC Motor Control - h-bridge pulsing strategy?
I did some more reading. It looks like the optimal is #1, but with a complementary PWM output used to switch on the high side's low FET during the OFF time. This is synchronous rectification, and it is more efficient because the windings are connected to a lower resistance during the off period.

Details can be found in the user manual for TI's Black Jaguar motor controller.