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