Response to some comments:
I'll leave the jury out on what kinda voting method to use in the finals, but I do want to say that an initial screening is just oh so important to avoid the, as someone put it, walk-out-of-the-room videos. While it may suck for the person getting not shown, this is a convention contest and thus is for the entertainment of the fans in the auditorium during the showing, and making 1/2 of them want to leave isn't a good thing.
As for prizes, I would say that the best prize I got was the little crystal trophy thing from AX, followed VERY closely by the cool clapboard given out by SakuraCon for my SC2000 win. They both were very cool, and I think that more than DVDs or what not is what I would want if I won another contest. I'm not in it for the monetary compensation when I enter to a contests, so DVDs or DVD players aren't really important to me. BTW, I'll bet you lots of creators already have DVD players, and region free ones, too. It's like giving a free paint brush to someone winning an art contest.
Contact Quu if you want the authority on the technical side of running a contest, but I'll say that the effort of dealing with digital submissions is not something I would recommend undertaking.