Step

With this interactive physics simulator, you place some objects on the screen, add some physical forces, and then see how they interact. It covers classical mechanics, particles, springs, gravitational and coulomb forces, collisions, molecular dynamics, and much more. (Note that in order to use Step on Windows, you'll have to download KDE for Windows.)

Jmol

Java-based Jmol gives you a 3D view of molecules with features for chemicals, crystals, materials and biomolecules. In addition to the downloadable version, it's also available as a Web app or in a development tool kit.

Kalzium

Kalzium describes itself as "your digital replacement for the periodic table on paper." It displays information from the periodic table in a variety of ways, and it offers a molecular weight calculator, 3D molecule editor, an equation solver for stoichiometric problems and more. (Note that in order to use Kalzium on Windows, you'll need KDE for Windows.)

Chemitorium

Open Source Tool for Science Education

Open-source molecular builder, visualization and analysis tool. With Chemitorium you can create and edit structural formulas of organic compounds, and vire them in three-dimension. The results can be exported in various formats as picture or video file.