Chemical and Structural Databases

ChemSpider
Text or structure-based chemistry information, spectra and properties from the Royal Society of Chemistry.
NIST Chemistry WebBook
Thermochemical data and spectra from the National Institute of Standards and Technology.
USDA Nutrient Database
Energy content of a wide variety of foods from the United States Department of Agriculture. Enter keyword (e.g. peanut or corn puff) and press return. Then click on the report button (a 100 g sample size is convenient.)
Pubchem Compounds
Free repository non-curated database of 100 million chemical molecules.
Protein Data Bank
Open-access repository for the 3D atomic structures of proteins, DNA, RNA, and their complexes.
Cambridge Crystallographic Data Centre
Repository for small molecule organic and metal-organic crystal structures. Structure publications include the CCDC code as supporting information.
Crystallography Open Database
Open-access crystal structure repository for organic, inorganic, metal-organic compounds and minerals.
American Mineralogist Crystal Structure Database
Crystal structure database focused on minerals and solids of interest to mineralogists.
Virtual Museum of Minerals and Molecules
Important molecules and minerals in soil and environmental sciences.
Database of Zeolite Structures
Repository for framework types from the Structure Commission of the International Zeolite Association.
FDA DailyMed
FDA labels and package inserts of marketed drugs for each brand name.
DrugBank
Drug data and drug target (i.e. sequence, structure, and pathway) information.
Chemical Entities of Biological Interest (ChEBI)
Dictionary of small chemical compounds from the European Bioinformatics Institute. Select the stars option (manually curated data.)

Other Sources

Total Syntheses
Name reactions, organic synthesis search by transformation, protecting groups, and total syntheses
ChemSpider SyntheticPages
Interactive database of synthetic chemistry hosted at the Royal Society of Chemistry. "We publish practical and reliable organic, organometallic and inorganic chemical synthesis, reactions and procedures deposited by synthetic chemists. Synthetic methods on the site are updated continuously by chemists working in academic and industrial research laboratories. ChemSpider SyntheticPages encourages submissions from graduate students, postdocs, industrialists and academics."
Molbank
One compound per paper (Open Access Journal)
Compound Interest, Andy Brunning, Cambridge University
Graphics information about everyday chemicals, often published in C&EN.
Molecule of the month, Paul May, Bristol University
Monthly molecules since 1996

Journals