The vast majority of the money is going to organizations that provide services to low-income people.
If you are looking for non-profit ideas that help the kind of giving I do, check out Razoo. Another thing those organizations could use is a way to lower operational costs, potentially by pooling with others.
Current projects: http://nlnet.nl/project/current.html
The only charity I support that I suspect anybody will have heard of would be the RNLI (Royal National Lifeboat Institution; the folks that go out and rescue people at sea http://en.wikipedia.org/wiki/Royal_National_Lifeboat_Institu... )
Usually I donate once a year to my chosen three charities, bot sometimes there will be a small bonus at random times.
It's basically Kiva for india.