Union of Concerned Scientists uses scientific analysis to shed light on environmental issues. MIT students and faculty founded UCS in 1969 to prevent the abuse of science and technology.
Resources for the Future conducts independent research -- rooted primarily in economics and other social sciences -- on environmental and natural resource issues. You can access their research through their site -- great information!
Bioneers brings scientists all over the world together in an effort to restore the Earth.
Northwest Environment Watch publishes their research on issues affecting the northwest North America.
The Science & Environmental Policy Project researches climate issues.
Public Policy Associates does research on a variety of environmental and economic issues.