BKchem - BKChem is a free (as in free software :o) chemical drawing program.
ChemDraw - ChemDraw - The Gold Standard for Chemical Structure Drawing and Research Publications.
pymol - PyMOL is a powerful and comprehensive molecular visualization product for rendering and animating...
ACD/ChemSketch - ACD/ChemSketch for personal and academic use brings the power of our structure drawing package to your home computer.
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: