Charity Navigator seems to be based on the 990 alone. Their methodology is here:
Charity Navigator's Methodology : Charity Navigator
Charity Watch, another charity rating service, analyzes many documents besides the 990. Their methodology is here:
Criteria & Methodology | Charity Ratings | Charity Rankings | CharityWatch
Charity Watch explains how some charities try to make it look like they are more efficient with donations than they are and how Charity Watch looks for that and uses it in its evaluations.
Keep in mind that both Charity Watch and Charity Navigator are 501c3 charities themselves but neither rates the other.
