Molecular Workbench is a free and open source site with some really nice interactive simulations in science.
There are hundreds of simulations in physics, chemistry, biology, biotechnology and nanotechnology. There are embedded assessments and the ability to create your own simulations and even create modules with text, simulations and more all together.
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It is a download for Windows, OS X and Linux and they are creating the next generation of simulations using HTML5 so they can be used online. Google is helping them with this.
http://mw.concord.org/nextgen/#interactives
Take a look - there are some great activities on here.
Related:
PhET - excellent, free, virtual labs and simulations for science - new materials available