On a personal level I don't think there's any real future in prizes donated by others offering of any real incentive for people to enter these contests - fan fiction is by its very nature a labour of love for want of a better term, not something that is done for any sort of a reward.
Perhaps I'm throwing a curve-ball in here, or completely off the mark, but does anyone else think there is any mileage in the idea that the concepts being generated by winners might be a little TOO open? For example concepts like "revenge" or "betrayal" are sometimes so wide in their scope that it can be difficult to distil down into an actual story?
Could a more narrow concept help focus the mind? Something like "your chosen crew answers a distress signal from a vessel thought lost a century earlier, but they are not the only ones to have responded..."