Avogadro - Avogadro is a free, fantastically easy to use molecule editor.
ChemDraw - ChemDraw - The Gold Standard for Chemical Structure Drawing and Research Publications.
BKchem - BKChem is a free (as in free software :o) chemical drawing program.
GPeriodic - GPeriodic is a periodic table application for Linux.
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.
pymol - PyMOL is a powerful and comprehensive molecular visualization product for rendering and animating...