American Civil Liberties Union (ACLU) Probably the largest and most well-established organization actively working on a broad range of issues related to individual rights.
The First Amendment Center of the Freedom Forum provides excellent information on a wide range of topics related to all aspects of the First Amendment, including freedoms of speech, religion, press, petition and assembly.
The Institute for Justice A public interest law firm "in the courts of law across this country winning cases preserving freedom of opportunity and challenging government's control over our lives." Specific areas of litigation include economic liberty, first amendment, school choice, private property rights and civil rights.
The Electronic Frontier Foundation You may not realize it, but there's a battle underway that will determine your rights in the digital future--and this organization is leading the charge. Areas of focus include anonymity, censorship, consumer rights, copyright law, filtering and surveillance.
The Foundation for Individual Rights in Education (FIRE) , an organization devoted to free speech, individual liberty, religious freedom, the rights of conscience, legal equality, due process, and academic freedom on our nation's campuses.
Public Citizen , a consumer advocacy organization founded by Ralph Nader in 1971, works for "openness and democratic accountability in government, for the right of consumers to seek redress in the courts; for clean, safe and sustainable energy sources; for social and economic justice in trade policies; for strong health, safety and environmental protections; and for safe, effective and affordable prescription drugs and health care." The site includes a page on Internet free speech.
The Open Directory Project page on Human Rights and Liberties provides a listing of web sites on a variety of rights, including free speech, parents' rights, privacy, women's rights and youth rights.
Gigalaw.com This site provides an extensive collection of useful articles on a wide range of legal subjects, including free speech, privacy, copyright law and Internet law (under the "miscellaneous" heading).
Legal Information Institute at Cornell Law School Comprehensive collection of legal information--federal and state constitutions, codes, laws, etc.