I greatly admire these groups:
Liberty:
Electronic Frontier Foundation, American Civil Liberties Union
Peace:
Christian Peacemaker Teams, AFSC/PCUSA/BPF
Non-human concern:
Animal Legal Defense Fund
Education:
One Laptop Per Child, ahumanright, OSI/FSF, Students for Free Culture
Medical:
Direct Relief International
Development:
Open Source Ecology, charity: water