Blender is a free 3D animation studio. It includes tools for modeling, sculpting, texturing (painting, node-based shader materials, or UV mapped), UV mapping, rigging and constraints, weight painting, particle systems, simulation (fluids, physics, and soft body dynamics and an external crowd simulator), rendering, node-based compositing, and non linear video editing, as well as an integrated game engine for real-time interactive 3D, and game creation and playback with cross-platform compatibility.
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.
PLIB is a set of libraries to write games and other realtime interactive applications that are 100% portable across a wide range of hardware and operating systems. It's used by Majik3D, FlightGear, and others, and includes libraries for GUI widgets, sound replay, geometry, scene graph, joystick, and fonts/text.
MayaVi is a free, cross platform, easy-to-use scientific data visualizer. It provides a powerful GUI to ease the visualization process. It is written in Python and uses the Visualization Toolkit (VTK) for the graphics. MayaVi can be scripted from other Python programs and also from the interactive Python interpreter. MayaVi includes the VTK Pipeline browser. The VTK Pipeline browser is a Python module (vtkPipeline) that enables one to view and configure the objects in the VTK pipeline graphically with a Tkinter-based GUI. The browser should work for any Python script that uses VTK. MayaVi also provides classes to pickle a VTK object and a simple class documentation browser.
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.
libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers. It provides some of the typical 3D viewer functionality, such as the ability to move the camera using the mouse, which is lacking in most of the other APIs. Other features include mouse manipulated frames, interpolated keyFrames, object selection, stereo display, screenshot saving, and much more. It can be used by OpenGL beginners as well as to create complex applications, being fully customizable and easy to extend. It ships with many examples and comprehensive documentation.