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Avogadro - Avogadro is a free, fantastically easy to use molecule editor.
ChemDraw - ChemDraw - The Gold Standard for Chemical Structure Drawing and Research Publications.
BKchem - BKChem is a free (as in free software :o) chemical drawing program.
ACD/ChemSketch - ACD/ChemSketch for personal and academic use brings the power of our structure drawing package to your home computer.
Gnome Chemistry Utils - The Gnome Chemistry Utils include six chemistry related programs:
pymol - PyMOL is a powerful and comprehensive molecular visualization product for rendering and animating...