Molecular Workbench is a free and open source system that provides visual, interactive simulations for science. The simulations are in lesson format, with embedded assessments and the ability to change variables and see what happens. There are hundreds of free simulations in physics, chemistry, biology, biotech and nanotech.
Some are similar to the simulations in PhET, but these are more lesson based vs. just a simulation. They are well written and designed and the interactive simulations really explain concepts well and let students explore them in more depth.
The other very cool feature is that educators can customize any of these simulations to better fit their lessons and you can use the software (free) to create your own from scratch using their modeling tools.
Here is a screen shot from the Heat and Temperature module. The introduction page has a simulation that shows molecular movement based on temperature.
Molecular Workbench is one of those resources that has a lot of potential. Teachers can use them as part of class, as extra help, or as an online course. Students could even use the software to create their own simulations and lessons as an assignment.
Related:
PhET - free online science and math simulations - very cool!