Concord Consortium, an educational non-profit, offers a free simulation program called Molecular Workbench, which can be used to learn many important concepts (e.g. intermolecular forces, molecular structures, states of matter, thermodynamics, reactions) in chemistry through cool simulations.
The main page to download the software is:
There is a virtual museum that collects scores of animations made from models:
The program is frequently updated. Check out the news at:
to see major development.