In order for community annotation efforts to succeed, they need to become part of the established research process: mine annotations, generate hypotheses, do experiments, write manuscripts, submit annotations. Rinse and repeat.
A thoughtful post by Todd Harris on his blog which lists some suggestions for how to fix the failure of community annotation projects.
I particularly like Todd's 3rd suggestion:
We need to recognize the efforts of people who do [community annotation]. This system must have professional currency to it, akin to writing a review paper, and should be citable…