I've been a fan of Heifer International for being a charity based on creating sustainable agricultural development in the third world while operating in an ethical fashion (lacking in most charities) that distributes more money to the people who need it, rather than squandering it in adminstrative fees (they operate at about 25% of funds going to fundraising and administration). When you see many charities with 95% administrative costs, you lose faith in the idea that giving money to charities is doing anybody any good.

Now we have a charity that ideologically I can support wholeheartedly, the Richard Dawkins Foundation for Reason and Science. It's still getting off the ground, but with any luck it will be managed in a similarly ethical fashion (my criteria is that less than 30% of donations may go to administration/fundraising).