I don't like comparing cons to other cons, and I don't want to give the impression that I think PortCon should emulate others cons - I think it has its own, awesome aesthetic, and PortCon should do things the PortCon way.
That being said, Otakon screens the AMVs for the contest by running through all the genres completely one at a time. I think they try to order the videos in such a way that there is enough difference between them - for instance, if there are two drama entries that use Death Note, they will have one at the beginning of the drama entries, and one at the end, and also some videos just have more "energy" than others, so they try to order them so the high energy videos are well distributed. I have never had a problem with watching the genres in clusters, and I think it's really the best way to do it. By the time the entire contest is over, it's a bit difficult to remember which video is which, but if it's just 5-6 entries in a given category, that makes me significantly easier.
Also, the ballots for the contest usually include the video source and song information. So if you don't remember the video name, you might remember it based on the song, or anime source(s).
Between the two of these, I think it will cause a lot less confusion and encourage voting. My friend didn't vote, because he couldn't be sure he was voting for the videos he wanted.
That being said, I greatly enjoyed the contest, and I think it was very well done. I just want to make sure it's even better next year!
Congrats to all the winners!