Someone correct me if I'm wrong on this:

Even if it is true that you can't produce any significant amount of additional power by pulling up on the pedals, I'd hypothesize that with the motion of pulling up, a clipless rider will be able to remove more weight from the ascending pedal than a rider on platforms. The rider on platforms will have to keep his foot planted in the correct position, and this results in a certain amount of pressure resisting the upward motion of the crank. If the rider is free from this concern and able to totally unweight the ascending pedal, more of his effort will be used in moving the bike forward.

So, whether there is an increase in overall power due to the upward motion or a decrease in wasted power, the net result is more power going to the ground.