breve - 3D swarm simulation environment (OS X and Linux).
framsticks - 3D evolution and simulation of artificial life (Windows).
Mirek's Cellebration - 1-D and 2-D Cellular Automata (Windows).
Lifelab - 1-D and 2-D Cellular Automata (OS X).
VMD - molecular visualisation (Windows, OS X and Linux)