The Foundation Beyond Belief is a new humanist charitable and educational organization that can be the focus of your godless giving. They’ve got an interesting approach: they set up 10 categories (education, the environment, poverty, human rights, etc.), and you pick what percentage of your donation you’d like to go to each category. They also highlight a reputable charity within each category that will receive your donation: read the FAQ for details on how it works.
One of the major virtues of this foundation to the humanist and atheist movement is that it can be (if many of us cooperate!) a center point that makes godless donations more prominent; it can also make the community of unbelievers a desirable group for charitable organizations to court. So join up! They do have a $9 annual membership fee, but it’s also a group that emphasizes the efficient distribution of your money to the people who need it most.