Avogadro

Avogadro is a beautiful molecule and material visualization and editing tool. It’s cross-platform and open source, produces high quality images and has some excellentscreencasts to help you get started.

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

Cross-Platform: Molecular builder/editor for Windows, Linux, and Mac OS X.
Free, Open Source: Easy to install and all source code is available under the GNU GPL.
International: Translations into Chinese, French, German, Italian, Russian, Spanish, and others, with more languages to come.
Intuitive: Built to work easily for students and advanced researchers both.
Fast: Supports multi-threaded rendering and computation.
Extensible: Plugin architecture for developers, including rendering, interactive tools, commands, and Python scripts.
Flexible: Features include Open Babel import of chemical files, input generation for multiple computational chemistry packages, crystallography, and biomolecules.

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.

Avogadro is an application purely for scientists and students that have to draw three-dimensional molecular compositions that showing a molecule from every conceivable angle and perspective.

It works across platforms and is used in computational chemistry, molecular modeling, bio informatics, material science and other related areas. The aim has been to make 3D molecular manipulation as easy as possible and even if your not a scientists, it's quite entertaining just creating your own different coloured structures that look good. This can be done simply by using the mouse buttons and dragging the molecules on their three axis. Probably the best aspect of this program for those with some coding knowledge is that it can be easily extended and developed via plugins. Avogadro is based on Open Babel according to the developers and in future, will also offer scripting options. The main problem you'll find is that like with many open source collaborations, it is prone to bugs and errors so it may crash at any time.