I directed my money to Humble Bundle themselves. I'm rather suspicious of how charity funds actually allocate their money.
One of my ex's worked at a charitable organization (cancer related). I was shocked at the posh gatherings and other little dos they had on a regular basis though this was explained to me as a way to attract more money from high income earners. They were audited every year by the government as a requirement to maintain their charitable status so there probably wasn't anything serious going on but they had some borderline expenses and things like good salaries, employee benefits, etc. You don't get rich working at them but many people seem to do alright, her salary there was almost as good as mine and her work was a lot less stressful. I remember someone at a party once posed the "what if cancer gets cured overnight?" question to several of the employees and they looked really uncomfortable, as if they took it for granted this was going to be a career forever. I suppose everyone worries about job security and they could probably just pick another cause to get involved with.
That's not to say they didn't do good work though. I think it depends a lot on the organization, I've seen some not-for-profit and charities that can barely sustain themselves.