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ChemDraw - ChemDraw - The Gold Standard for Chemical Structure Drawing and Research Publications.
Gnome Chemistry Utils - The Gnome Chemistry Utils include six chemistry related programs:
Avogadro - Avogadro is a free, fantastically easy to use molecule editor.
MolView - Open Source online service
ChemDoodle - Chemical drawing and publishing software for desktop, web and mobile. Affordable and used by thousands of scientists around the world. Free trial available for immediate download.
BKchem - BKChem is a free (as in free software :o) chemical drawing program.