Jmol

Jmol is a cross-platform Java-based program which lets you look at three-dimensional views of chemical structures. With it, the atoms that make up chemical compounds can be seen from almost any angle.

Jmol includes a desktop tool (Jmol) and a browser extension (JmolApplet) so you can take a look at particular molecular structures no matter where you are.

With Jmol, you can also generate webpages from compatible files and add notes to the 3D views, including measurements between atoms, its symbol, its number, and the names of the chemicals they represent.

You can animate and vibrate the molecular structures, as well. Jmol can generate the following output formats: JPG, PNG, PPM, PDF, and PovRay.