Chemical 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.)
ChemIDplus
Chemical structure, toxicity, and physical property searching from the National Library for Medicine.
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.)
Pubchem Compounds
Free repository non-curated database of 30 million chemical molecules.

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)

Journals