Jmol is a Java molecular viewer for three-dimensional chemical structures. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame files and computed normal modes from quantum programs. Note that this program can render small molecules as well as large molecules (i.e. proteins). A must-have for organic chemistry and bio-chemistry students out there.

http://repo.openpandora.org/?page=detail&app=jmol