MollyCule!

Marvin is a great alternative to the subscription based ChemDraw by CambridgeSoft. It is a collection of tools for drawing, displaying and characterizing chemical structures, substructures and reactions.It will also convert structures you create to various molecular visualiztion formats, such as .pdb and .mol, compatible with programs such as PyMOL and SwissPDB Viewer.

ACD/ChemSketch is a chemically intelligent drawing interface that allows you to draw almost any chemical structure including organics, organometallics, polymers, and Markush structures. Use it to produce professional looking structures and diagrams for reports and publications.

BKChem is a free (as in free software :o) chemical drawing program. It was conceived and written by Beda Kosata and is currently maintained by Reinis Danne.

Communicate with the natural language of chemical structures, biological pathways, and models