General

Math, Physics, & Chemistry - science.gov links for Astrophysics, Chemicals, Mathematical Modeling ...
Chemistry and Materials: Research Overview - looks at the sciences of stuff and some of the greatest challenges in the field today: understanding "emergence" (when the whole adds up to much more than the sum of its parts), creating new materials (high-strength plastics, superconductors, photovoltaic devices), mimicking products and processes of nature, and finding green ways to manufacture products, create chemical reactions, treat waste, and generate energy.
Chemistry - simulations of thermodynamics, states of matter, water, and reactions. See interactive visualizations of Brownian motion, diffusion and osmosis, ion transport, distillation, motion of greenhouse gases, liquid-solid comparisons, intermolecular forces, chemical reactions, explosion, and more. (National Science Foundation)

Focused

Chemistry and Chemicals - more narrow Science.gov links
Virtual Chemistry Library - NIST
Chemistry - links for general, analytical, biochemistry, chemical & petroleum engineering, inorganic/ crystallography, organic, photochemistry, and physical (Argonne National Laboratory)
Chemistry and Analytical Chemistry - databases and information

Understanding Our Planet Through Chemistry - how chemists and geologists use analytical chemistry
Quantum Chemistry - what it is

Ask-A-Scientist - Chemistry, archive 1991+
Chemistry WebBook - database of organic chemistry compounds, organized by species; contains chemical and physical property data (NIST)
Elemental Data Index - organized by element (NIST)
Atomic Weights and Isotopic Compositions - for elements 1 through 111 with isotopic compositions or abundances
Periodic Table of the Elements (Los Alamos National Lab)

ChemLinks Coalition - offers resources for the first 2 years of college chemistry; topics include global warming, ozone, fats in our diet, computer chip thermochemistry, making water safe to drink, what's in a star, acid rain, reducing air pollution from automobiles, copper, & building a better CD player (getting light out of a solid).
ChemTechLinks - features resources for training chemical technicians: instructional materials, industry standards, professional development opportunities, chemical technician careers & salaries, molecule of the week, chemistry in the news, a newsletter, & answers to questions such as "Why are some schools considering a ban on soda machines?"