ChemTube3D is a website maintained by the University of Liverpool that has interactive 3D animations ans structures.  The content is broken up into several areas:

• A Level;
• Organic Reactions;
• Structure and Bonding;
• Polymers;
• Solid State.

There is a lot of information on the site, and the information could be used in many courses.  The areas that I find most useful in my sophomore-level inorganic chemistry course.

• Structure and Bonding -> Simple Molecular Orbitals
• Solid State

I use the solid state animations in lecture and I encourage my students to use these when studying.  My students find these visualiztions quite useful.

In my advanced half-semester course in organometallic chemistry, I use and refer my students to the "Organometallic Chemistry" and "Enantioselective metal catalysts" (found the "Organic Reactions" section).