CSD - Cambridge Structural Database System and the related Mercury, ConQuest, SuperStar, IsoStar, and Mogul programs.
RTAM - Bibliographic database of relativistic calculations on atoms and molecules.
NIST Chemistry webbook- Structures, spectra, properties.
Pubchem, hosted by NCBI - Structures, properties, structural searches, etc.
PDB Protein Database
ZINC - A free database for virtual screening - Structures, properties, structural searches, etc.
Chemspider - Structures (2D, 3D), properties, structural searches, etc.
Spectral Database for Organic Compounds SDB - NMR, IR, Raman, etc. spectra from a Japanese database.
MassBank - High Quality Mass Spectral database
Crystallography Open Database - a collection of organic, inorganic and complex crystal structures
Espacenet Patent database (in Finnish)
United States Patent and Trademark Office Patent database
eMolecules Structure searchable database with some 8 million unique chemicals
Chemical Structure Lookup Service some 30 million molecules hosted by NIH
CRC Traditional reference handbook with tabular data, formulae and trivia
NOMAD CoE NOvel MAterials Discovery Laboratory - a searchable database on computational materials data