ChemDraw - ChemDraw - The Gold Standard for Chemical Structure Drawing and Research Publications.
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...
BKchem - BKChem is a free (as in free software :o) chemical drawing program.
SketchBook - SketchBook is a professional drawing or painting application that allows designers, architects, and concept artist to sketch their ideas and create adorable illustrations in no time.