When you buy something from the Humble Bundle you can select that the whole amount from the sale goes to charity. But does your whole amount really get sent to charity, or is some of it taken for administrative purposes etc. by the Humble Bundle team?
I'm sure it's all going to charity. There's a separate slider to allow money to be send to Humble Bundle itself, because they need to pay their servers and lots of other stuff of course. This is why I don't think some of the money is send to Humble Bundle unless this slider isn't at it's zero position. When you set this slider (and the slider for the developers) to the zero position, and the charity slider to 100%, I'm sure everything you pay is send to charity.
I'm not able to verify this though, because I'm unable to look into the code of the website. You can always ask the same question on the Humble Bundle site itself!