[url=http://www.povray.org/]POV-Ray[/url] is a free 3D graphic program. May be it can be used to create 3D scene from data generated by EJS.
But some of the scenes at http://web.ncf.ca/ch865/ site, can be generated from EJS directly. I will try to create some simulations similar to those shown at the web site. If you download EJS, you will also find some 3D examples.