"Charity Navigator, America's premier independent charity evaluator, works to advance a more efficient and responsive philanthropic marketplace by evaluating" over 5,000 of America's charities.
The "donor's guide to the charitable universe", is a project of Philantropic Research Inc. Contains some information on 620,000 nonprofits. GuideStar powers the popular Internet guides NetworkForGood and JustGive.
JustGive is a nonprofit organization whose mission is to connect people with the charities and causes they care about and to increase overall giving. Donations may be made from this one site.