Talk about transparency. GiveWell.net which just launched, and which I wrote about here, uses community reviewers to assess giving opportunities for donors. They've developed and posted their criteria for these reviews. The ratings process includes criteria and scoring on these parameters:
Strategies and Activities
Evidence of effectiveness
Reviewers also post "unanswered questions" and a list of the sources they used to create their ratings. A more complete description of the process is found here. GiveWell maintains a blog here.