Cambridge Structural Database (CSD)

CSD is a repository for small-molecule organic and metal-organic 3D crystal structures, containing over 875,000 entries from x-ray and neutron diffraction analyses.

American Mineralogist Crystal Structure Database

Includes every structure published in the major mineralogy journals. Search by mineral, author, element names, cell parameters, etc. Here's a description from the journal.

Bilbao Crystallographic Server

Crystallographic database and programs aimed at analyzing, calculating and visualizing problems of structural and mathematical crystallography, solid state physics and structural chemistry.

Crystallography Open Database (COD)

Open-access collection of crystal structures of organic, inorganic, metal-organic compounds and minerals, excluding biopolymers.