Rationalism, Freethought and other thought-full links:

2think.org: Science, philosophy, skepticism and so on.
Adbusters Media Foundation: Anti-corporate media organization that makes uncommericals... a great site!
AHA: American Humanism Assoc.
Allen Sokal: Physicist who embarrassed the po-mo crowd with his published spoof in Social Text.
The Anti-Evolutionists: William A. Dembski: Details on The Sagan Society's new favorite creationist.
Atlanta Freethought Society: Atlanta's Excellent Freethought Group. 
BARF: The Biblical America Resistance Front.
BRS: The Bertrand Russell Society. 
CSICOP: Committee for the Scientific Investigation of Claims of the Paranormal.
Campus Freethought Alliance: Just what it says.
Common Sense: Princeton's Secular Society.
Critical Thinking: The Center for Critical Thinking. 
The Edge: Big time brain food.
FAIR: Fairness and Accuracy in Reporting - and do we ever need it!
The Foundation of Humankind, Inc.: A secular humanist non-profit resource center.
Freedom Forum: A 1st Amendment Organization. 
Freedom From Religion Foundation: Church & State -- Keep 'em separated! (Of special note is this Freethought Today article on movies with freethought themes or characters.)
James Randi: The James Randi Educational Foundation. 
No answers in Genesis: A collection of writings and resources on Evolution.
Overlawyered.com: Title says it all.
Pierre Stromberg's Paranormal Northwest: A skeptic site for Washington State.
Prometheus: A magazine for thinking persons.
Rationalism: The Rationalists of E. Tennessee. 
Reasonworks: Audiotapes for the Freethinker.
Secular Student Alliance: "Mobilizing Students for a New Enlightenment" is a great slogan, isn't it?
Secular Humanism: The Council for Secular Humanism.
The Secular Web: Proud to name themselves Internet Infidels.
Skeptics Society: Michael Shermer's Skeptic Magazine.
SKEPTICS.CAnada: Ontario Skeptics, the largest skeptic group in Canada.
Social Issues Research Centre: Critical examination of the media on health issues from the U.K.

Science-oriented links:

American Astronomical Society: Publishes the Astrophysical Journal.
The American Scientist: A Scientific Research Society.
Bad Science: Fighting the battle of misinformation. Bet you don't know why fog really forms!
Center for Science in the Public Interest: Publishes the Nutrition Action Newsletter. 
The Foresight Institute:   Dedicated to preparing for nanotechnology.
The Genome Database: The world human Genome project. 
The hmsbeagle A BioMedNet Magazine.
Hubble Heritage: High art from the Hubble Space Telescope.
The IG Nobel Prize Home Page: The prize for research that cannot or should not be duplicated. 
JAMA: Journal of the American Medical Association. 
Morbidity and Mortality Weekly Report: Sounds bad, huh? Don't be fooled, this is an excellent journal. 
NASA: Our destiny in space.
NCSE: National Center for Science Education. 
National Academy of the Sciences
The National Institutes of Health: Our Nation's research center. 
Nature: International Journal of Science.
New England Journal of Medicine: Weekly journal of the Massachusetts Medical Society. 
New Scientist: Superb weekly science journal from the U.K.
NIX: The NASA Image Exchange.
The Nobel Prize Internet Archive: Check here to find out if you're a winner.
The Planetary Society: Space geeks unite!
Quackwatch: Your guide to health fraud, quackery, and intelligent decisions. Terrific resource, lots of links.
Science Online: American Assoc. for the Advancement of Science. 
Scientific American: The Scientific American Magazine.
String Theory: The Official String Theory Website. 
UGA Observatory: Schedules monthly telescope nights.
The Why Files: The Why files at the University of Wisconsin.