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.
pymol - PyMOL is a powerful and comprehensive molecular visualization product for rendering and animating...
Gnome Chemistry Utils - The Gnome Chemistry Utils include six chemistry related programs:
Jmol - Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry...