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Avogadro - Avogadro is a free, fantastically easy to use molecule editor.
ImageJ - and Other Health Care
BKchem - BKChem is a free (as in free software :o) chemical drawing program.
ACD/ChemSketch - ACD/ChemSketch for personal and academic use brings the power of our structure drawing package to your home computer.
TrueChem - TrueChem is software designed specifically to control and automate the management of chemistries, coatings, and wet processes.
GPeriodic - GPeriodic is a periodic table application for Linux.