science

General & Reference

 * arXiv.org: "Open access to e-prints in Physics, Mathematics, Computer Science and Quantitative Biology"
 * HV Wiki: for "science, engineering, and technology, especially by hobbyists at home".

Issues

 * Issuepedia: Corruption in academia

Biological Sciences

 * BioForge: "a new community for biological innovation" (sort of like SourceForge, but for bioscience)
 * BioRoot: for information and materials sharing in the biological sciences
 * The Synaptic Leap: "Open-Source Biomedical Research"
 * Tree of Life taxonomy project
 * Wikiomics Bioinformatics Wiki

Mathematics

 * Free Electronic Mathematics Journals

Complex Systems

 * New England Complex Systems Institute
 * NECSI Complex Systems Wiki

Physics

 * not yet reviewed:
 * Celestia "free galaxy-simulator"
 * Motion Mountain "the free physics textbook"
 * Orbiter: "free (though not open-source) space flight simulator"
 * Space Combat "free, physics-based simulator"
 * Quantum Physics
 * explanatory series by Eliezer Yudkowsky at Overcoming Bias:
 * 2008-04-09 Quantum Explanations
 * 2008-04-10 Configurations and Amplitude
 * 2008-04-11 Joint Configurations
 * 2008-04-12 Distinct Configurations
 * 2008-04-15 Classical Configuration Spaces
 * 2008-04-15 The Quantum Arena
 * 2008-04-17 Feynman Paths
 * In the beginning was the bit: Anton Zeilinger's information-theory-based explanation

Organizations

 * Society for Amateur Scientists: "Helping ordinary people do extraordinary science"