Free for Education Applications : that work in Stereo:

Astronomy

Partiview:
A digital planetarium, produced by the Hayden Planetarium and supports stereo visualisation:
Partiview Application
Cosmus: more datasets for Partiview
Seldon's Partiview Resources

Molecular Modelling

Pymol:
An excellent molecular modelling program that supports stereo visualisation:
PyMol Application
PyMol Links
An Introduction to PyMol

Free for Education Applications : others:

3D Modelling

Blender:
A very powerful, but not the easiest, 3D modelling program:
Blender Application
Blender Tutorials
Blender Blog
The Blender Model Repository

Wings 3D:
A subdivision modelling program:
Wings 3D Application
Wings 3D Tutorials

Art of Illusion:
A subdivision modelling, animation and rendering program:
Art of Illusion 3D Application
Art of Illusion Help

POV-Ray:
A modelling, and ray tracing rendering program:
POV-Ray 3D Application
POV-Ray resources

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