Avogadro - Avogadro is a free, fantastically easy to use molecule editor.
ChemDraw - ChemDraw - The Gold Standard for Chemical Structure Drawing and Research Publications.
Gnome Chemistry Utils - The Gnome Chemistry Utils include six chemistry related programs:
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.
MolView - Open Source online service
pymol - PyMOL is a powerful and comprehensive molecular visualization product for rendering and animating...