DX - Open Visualization Data Explorer is a visualization framework that gives users the ability to apply advanced visualization and analysis techniques to their data.
GDIS - a GTK based program for the display and manipulation of isolated molecules and periodic systems.
GDPC - a program for visualising molecular dynamic simulations, it is a very versatile program and could easily be used for other purposes.
gOpenMol - A visualization toolbox for molecular structures and trajectories.
Molekel - an interactive, three-dimensional molecular graphics package.