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.
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...