Periodic table: Webelements

Searchable database on things chemical: Chemfinder

Conversion factors: NIST

Pictures of materials-related stuff: Caspar Fall's Homepage

The Joannopoulos Research Group at MIT

Tomas Arias's Reasearch Group at Cornell

Software for molecular structures: RasMol, Chime, and Protein Explorer

Classical molecular dynamics package: AMBER

Protein Data Bank: PDB