The only issue with charitynavigator, which Ben reports on, is that it only reports charities that receive more than $500,000 in public support with require 4 years of Forms 990 to complete an evaluation.
Ours usually is usually between $50 - $100K (as 90% of our work is pro-bono) and as a small organization less than 1% is spent on admin. - I don't take a salary and cover administrative costs.
I think Network for Good/Guidestar is more inclusive but there support sucks (online updating has been down for FOUR months and no-one returns calls).
Brainstorming here ... but what would be most useful would be a system that that incorporated elements from Ebay and Amazon.
Allow donors and recipients to rate each other. Ask the community -- were they impressed by the charitable donations?