http://freethoughtpedia.com/wiki/CharitiesUseful.
I do have some questions with the "development" oriented ones (because the assumption that industrialization cures all ills is just empirically wrong), but as I said, one issue at a time, and there are a lot of good charities here.
Not just the ACLU-- it's easy to find a lot of political groups that are not religious, but help-the-poor type charities too.