Avogadro - Avogadro is a free, fantastically easy to use molecule editor.
BKchem - BKChem is a free (as in free software :o) chemical drawing program.
ImageJ - and Other Health Care
GPeriodic - GPeriodic is a periodic table application for Linux.
TrueChem - TrueChem is software designed specifically to control and automate the management of chemistries, coatings, and wet processes.
pymol - PyMOL is a powerful and comprehensive molecular visualization product for rendering and animating...