Food & Water Watch
Focuses on food and water safety, but they also are at the forefrontof the anti-fracking movement and recently (2017) started a campaign to push for 100% renewables by 2035 (see also: Off Fossil Fuels Act by Rep. Tulsi Gabbard). Does not take corporate or government funding -- they explicitly call out the Waltons and ALEC, etc here. One of their main themes is fighting corporate control of food (e.g. factory farming and monocultures) and water supply (e.g. Nestle) by supporting activism and litigation against various attempts at privatization or regulatory rollback. They are my environmental charity of choice.
Constitutional Accountability Center
Defends a progressive reading of the Constitution via research and amicus briefs to key lawsuits. Some of their main focus areas are in fighting back against corporate personhood, defending environmental regulations and citizenship rights
Asian Pacific Environmental Network
Local political engagement (Richmond, Oakland) to support disadvantaged and low income immigrants or ppl of asian heritage. They have two main prongs of social and economic justice (e.g. opposition to Prop 13) and support for climate change action (opposing AB 398, import of tar sands, etc). Particularly focused on the Chinese community in the bay area, as well as some Laotians who live near a Chevron plant. They also do a lot of voter registration and engagement.
Rainforest Action Network
An environmental (justice) charity that focuses particularly on the ill-effects of deforestation (e.g. palm oil in Indonesia) and the effects of fracking and coal on the environment. They explicitly call out support for indigenous peoples (keystone xl, rainforest), and have an anti-corporate bent, particularly around the finance of projects that violate their core environmental principles. Their strategy roughly revolves on five-year time scales, during which time they identify projects and issues and work towards influencing the actions of multinationals such as Nestle (re: deforestation to support palm oil farming in Indonesia) and Chase (re: funding tar sands expansion).
American Civil Liberties Union Foundation, Inc.
First amendment rights powerhouse. This comes with pros and cons, among which include support for the KKK's right to free speech (even if I support their right to speech, not sure if I want my money going to their defense) and partial support for Citizen's United (https://www.aclu.org/other/aclu-and-citizens-united). In a post-Trump world, however, I think the good they can do outweighs this potential "cost".
NAACP Legal Defense & Educ Fund Inc
Probably the model organization for legal advocacy in the country. If anyone is going to protect minority voting and other rights, it will be them (check out their extensive case list: https://en.wikipedia.org/wiki/NAACP_Legal_Defense_and_Educational_Fund#Well-known_cases). They're getting a large chunk of my charitable contributions.
End Rape On Campus Inc
I support End Rape on Campus because they pursues direct, legal action to support survivors, including Title IX complaints, as well as funds educational action to enhance consent culture.
Mexican American Legal Defense and Educational Fund
One of the charities featured in Last Week Tonight: https://youtu.be/-rSDUsMwakI?t=19m4s
National Womens Law Center
Umbrella women's advocacy organization that promotes, among other initiatives, equal pay in the work place, enforcing fairness in classrooms (https://nwlc.org/wp-content/uploads/2016/11/final_nwlc_NOVO2016Toolkit.pdf) and women's health.
John S. and James L. Knight Foundation, Inc.
Supports journalism and community building through grants. I see them primarily as a resource for identifying good candidates for my money to support the free and independent press http://www.knightfoundation.org/articles/how-you-can-advance-quality-journalism-by-supporting-the-knight-news-match