AeroSpaceGuide by Vic Stathopoulos. Numerous space-exploration and solar-system related pages, very well done.
American Elements: Online handbook of the chemical elements (American and otherwise) from a large advanced materials producer.
Astrobites: The astro-ph Reader's Digest Written by postgraduate students: one paper a day from the astro-ph section of arXiv, retold in a form meant to be accessible to non-specialists.
Bill Beatty's Science Hobbyist: Much more than the name suggests.
Chembites: Written by postgraduate students. Summaries of recent research papers in chemistry, in a style meant to be accessible to non-specialists.
Chemistry Teaching Resources Annotated: Comprehensive and well-designed index by Knut Irgum. Unfortunately, a number of the links have expired.
DIY Physics by David and Shanni Prutchi
David P. Stern's Website: Presents a great deal of physics, astronomy, and space-science at approximatley high-school level, with cultural context. Parts of the site also feature lesson plans for classroom use.
Egglescliffe's Physics Pages: Andy Gregory's site, aimed at A-level (in the British sense) physics students. Egglescliffe is a school in Teesside, England.
Engineering Degree Resources: Information on a wide variety of subjects directly or very indirectly connected with engineering, ranging from Python programming to the life of Stephen Hawking. [EngineeringDegree.Net]
Free Book Centre: Physics Books: Links to e-books, including many lecture notes.
FreeScience: Hundreds of online technical-books.
Free Software Foundation: Heroes of our times.
GA-Net: Clifford-algebra news.
Gonit Sora: An ambitious online magazine about mathematical science. (Most articles are in English, but some are in Assamese.)
Handbook of Space Astronomy and Astrophysics (3rd edition) by Martin V. Zombeck [Cambridge University Press, 2007] Classic reference work. The Supplementary Web Links section lists hundreds of other sites in a logically organised fashion.
HEPStructure: Hierarchical index to the most cited papers at SLAC/SPIRES.
Igor Ivanov's PHYSICS ENCYCLOPEDIA @ Net Advance of Physics: A collection of annotated links to physics sites of interest, organized by topic. Not currently updated.
Internet Archive Vast number of books etc.
Internet Encyclopedia of Science by David Darling
Journal of High Energy Physics: A peer-reviewed free online journal.
Living Reviews: Peer-reviewed free review journals in various fields, including relativity and solar physics.
MathOverflow: Problem site for advanced mathematics.
n-Lab: "A wiki-lab for collaborative work on Mathematics, Physics and Philosophy, especially insofar as these subjects are usefully treated with tools and notions of category theory."
Net Advance of Physics RETRO Recommended Links: Pages dealing with the history of physics, mathematics, and astronomy, especially in the Nineteenth Century.
Physics: "Selections from Physical Review and Physical Review Letters explained for students and researchers in all fields of physics."
Physics StackExchange: Problem site for advanced physics.
Physics Update: News from the magazine Physics Today.
PlanetMath: Mathematics encyclopædia.
Random Integer Generator [Random.Org] Using atmospheric noise rather than an algorithm.
Resources for Chemistry Educators by Stephen Lower [Simon Fraser University] Very extensive.
Rod Nave's HyperPhysics: A complete undergraduate physics course in flashcard format. (Georgia State University)
Rusin's Mathematical Atlas: Articles and links in all areas of mathematics.
SETI@home: Serious project to "harness the spare power of hundreds of thousands of Internet-connected computers" to analyse the Berkeley SERENDIP radio data.
Shadow and Substance: "A website to display popular astronomy both visually and entertainingly."
Skulls in the Stars: "Dr. SkySkull" is the pseudonym of a physics professor at UNC. "The blog covers topics in physics and optics, the history of science, classic pulp fantasy and horror fiction, and the surprising intersections between these areas."
Spectrum of Physics: A comprehensive general physics links site.
Super Physics: Accessible non-mathematical introductions to some areas of modern physics.
Topics in Theoretical Physics by Luca Bombelli [University of Mississippi]
viXra: The anti-arXiv. Lots of noise, but some valuable signal.
Lecture Series on Core Quantum Physics (31 Lectures) and Classical Physics (38 Lectures) by Prof. V. Balakrishnan, Department of Physics, Indian Institute of Technology, Madras are available on YouTube.