Avogadro - Avogadro is a free, fantastically easy to use molecule editor.
Gnome Chemistry Utils - The Gnome Chemistry Utils include six chemistry related programs:
BKchem - BKChem is a free (as in free software :o) chemical drawing program.
Kalzium - Kalzium (German for: Calcium) is a periodic table of the elements for KDE SC 4.
ChemDraw - ChemDraw - The Gold Standard for Chemical Structure Drawing and Research Publications.
ACD/ChemSketch - ACD/ChemSketch for personal and academic use brings the power of our structure drawing package to your home computer.