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Many peace and justice organizations can be found here: http://www.en.wikipedia.org/wiki/Arab-Israeli_peace_projects
Organizations I know of that aren't included in that list: Zochrot, Adalah, New Profile, Breaking the Silence, Sheik Jarrah Solidarity, Nonviolence International, Israeli Committee Against Housing Demolitions, Machsom Watch, Palestinian Freedom Riders, Anarchists Against the Wall, and Rabbis for for Human Rights.
I'm by no means an expert on this subject, nor do I live in the area, so please feel free to correct me or contribute! (contact BlackGreenWhite)