pymol - PyMOL is a powerful and comprehensive molecular visualization product for rendering and animating...
Jmol - Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry...
Avogadro - Avogadro is a free, fantastically easy to use molecule editor.
VMD - Visual Molecular Dynamics - VMD - Visual Molecular Dynamics, molecular graphics software for MacOS X, Unix, and Windows
QuteMol - QuteMol is an open source (GPL), interactive, high quality molecular visualization system.
ChemDraw - ChemDraw - The Gold Standard for Chemical Structure Drawing and Research Publications.