Charity Navigator

Charity Navigator http://www.charitynavigator.org/ This organization ranks and categorizes charities for public navigation. 

The site is very user-friendly and I personally found the "Donor Advisories" list very helpful. This website chooses to warn donors of the listed charities for  "...a variety of reasons such an investigation by the Attorney General, a lawsuit against the charity and an atypical item of a significant nature reported on the Form 990." The presence of the charity remains on this list for a minimum of a year and the rating is removed. The site also has a "CN Watch List" which shares with donors that Charity Navigator has become "aware of conduct that may affect a donor's decision to support that charity" until the issue has been resolved. The rating remains in place. 

This website also has fun "top-ten lists" of various themes. For example, in the "10 charities in deep financial trouble" list you'll find insolvent charities working with negative network capital--their liabilities exceed their total assets. These charities are in a very dangerous position. 

The methodology behind this site is transparent: sharing reasons behind their rating system, age of ratings and a glossary of terms.