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.

Avagadro

Open Source Molecular Editor

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture.