I'll throw my opinion hat into the ring...
I would say that voting directly on any setting propasal should not be done directly, but instead should be done in a representative fashion. That, of course, means that the community should pick the actual submission judges by popular vote. The mechanic for picking the ENnies judges seemed to be a pretty good one. I also think that any judging should be about as blind as possible (which would mean closing and burying the thread where people are posting submissions).
Qualifications for the judges should include membership as an active member of the boards, and the judges should not be allowed to also enter the contest/search (that one is a no brainer).
Also, and this one would be directly for Morrus, I strongly suggest you make the restriction for entering this contest be that you are a full and contributing member of the community - and by that I mean paid membership. Not only will this thin the amount of submissions, but it will create an influx of money that can be used for administering the contest, as many (and I would include myself in this number) become paid members of the community.
Lastly, I hope you realize the immense amount of work that will end up being done by those who actually judge such a contest. If you decide to actually do this, you can pretty much count on saying goodbye to any kind of life!
And, once again, congratulations to those who made the first cut in the WotC search!