Jmol is a Free, Open Source molecule viewer and editor. It is a collaboratively developed visualization and measurement tool for chemical scientists. Jmol is an active project, and there are new features being added to it on a daily basis. Users are encouraged to modify it to fit their needs and to contribute their changes to the project.
The Chemistry Development Kit (CDK) is a library of Java classes for chemo-, bioinformatics, computational chemistry, and chemometrics. It provides important algorithms like substructure search, SMILES, Gasteiger charges, QSAR descriptor calculation, 3D structure generation, 2D layout and rendering, many IO formats, atom typing, and more.
JCGrid is a set of easy-to-use tools for real-world grid-computing. It doesn't require any file system sharing capability (such as NFS). It allows you to easily split a CPU-intensive task among several computers by using the JCGrid framework. Any file required for completing the task will be transferred by the framework. A cache is used in order to minimize file transfers. You can easily add or remove computers from the grid at runtime without losing any work. Support for POVRay is included as an example of use.
VisIt is an interactive parallel visualization and graphical analysis tool for viewing scientific data. Users can quickly generate visualizations from their data, animate them through time, manipulate them, and save the resulting images for presentations. VisIt contains a rich set of visualization features so that you can view your data in a variety of ways. It can be used to visualize scalar and vector fields defined on two- and three-dimensional (2D and 3D) structured and unstructured meshes. It was designed to interactively handle very large data set sizes in the terascale range, and works well down to small data sets in the kilobyte range.
CryptEngine is a fast 3D engine for Java. It is based on OpenGL and provides components and objects allowing the description and rendering of 3D scenes. Unlike several other 3D engines, it focuses on rapid application development and makes it possible to create and render complex 3D scenes without having to learn OpenGL. A large collection of demos are included, demonstrating the many features and providing you with valuable design techniques and tricks. It also facilitates game design with a sound system, scripting, and networking.
Vis/Space is a client-server system for visually exploring data structures in 3D virtual space. It allows the placement of various data sources in a three-dimensional environment. Custom search terms can be entered into a query field, or can be navigated to and from an existing object. All objects like images and "text screens" can be moved around. A single click on an image shows the full-resolution version in the foreground. Whole collections of images can be moved. A click to the cube also toggles among several different possible layouts. Data sources include search engines, microblogging, Wikipedia, image/video search, and 4chan.