ChemDraw - ChemDraw - The Gold Standard for Chemical Structure Drawing and Research Publications.
Avogadro - Avogadro is a free, fantastically easy to use molecule editor.
Jmol - Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry...
Gnome Chemistry Utils - The Gnome Chemistry Utils include six chemistry related programs:
UCSF Chimera - UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular...
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.