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The new name for the American Institute of Philanthropy is "Charity Watch." They have a short list of national shelter programs with a high rating (B or above). Here is the list.
Note that they do not endorse individual shelters in each city or town, but only umbrella organizations.
Charity Navigator has a list of 66 homeless shelters across the country that have a 4-star rating. Here is the list: http://www.charitynavigator.org/index.cfm?FromRec=1&bay=search.results&cgid=6&cuid=28&sortby=rtg
The BBB doesn't have national lists of homeless shelters to check out. They work in the opposite direction: you enter the name of a charity and they will tell you if they have information on it or not. There is more information here: http://www.bbb.org/
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