The Nature Conservancy and the Sierra Club are my go-to charities for the environment.
On a smaller scale, I donate money through Global Giving, which funds small-scale charitable projects around the world. I often seek out projects that focus on tree planting in deforested areas, or distributing solar-powered lanterns in developing countries (replacing dirty, polluting kerosene lamps). Also, I recently found out about Everybody Solar, which fundraises for solar-power installations in the U.S.
I don't know if this is the most effective way to donate, but at least it has a direct impact.