[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. 

VIEW or DOWNLOAD ejs xml source
then click to translate strings for selected locale.

Press the Alt key and the left mouse button to drag the applet off the browser and onto the desktop.