Open Source Solid Modeling CAD
BRL-CAD is a powerful cross-platform constructive solid geometry solid modeling system that includes an interactive geometry editor, ray-tracing for rendering & geometric analyses, network distributed framebuffer support, image & signal-processing tools.
PyMOL is an OpenGL based molecular visualization system
PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is free to everyone!
Ayam is a free 3D modelling environment for the RenderMan interface.
Earth orbits and coverage display in 3D on your laptop.
SaVi - simulate Iridium, Globalstar, O3b, Sirius Radio, GPS, Galileo and other satellite constellations, modify them, or design your own. Uses Tcl/Tk and Unix libraries; 3D viewing option requires Geomview running on X Window.