I like kaufman's idea. Actually I like whatever idea gets the most people the most playing time with the shortest wait. But as for seeding based on score -- there really aren't that many of us here judging. Surely there would be clusters of people who all got the same number of votes in the free-for-all round. In fact, what if, after a round like that, you had a scoring total like this:
Contestant A: 6 votes
B: 5 votes
C, D, E: 4 votes
F, G, H, I, J, K: 3 votes
L, M: 2 votes
And so on. Then how would you choose who got to advance?
Here's a potential solution which I suspect won't work: each judge gets a certain number of votes, and can split them between the contestants however s/he sees fit. Like I might get 50 votes, and give 35 of them to A, 7 to B, 5 to C, and 3 to D. Problem: the longer you wait to vote, the more control you have over the outcome. Solution: secret ballot. How? Either by having people e-mail the moderator, or asking Brad to code a ballot box. Both of these seem to me to be getting too complex, which is bad. I think the Comic Contest owes its longevity in no small part to its simplicity.
Don't mean to be a naysayer, just saying what comes into my head.
The what mentioned above is total fiction. Please don't take it seriously!