BRL-CAD is a powerful constructive solid geometry solid modeling system that includes an interactive geometry editor, ray-tracing support for rendering and geometric analysis, path-tracing for realistic image synthesis, network distributed framebuffer support, and image and signal-processing tools.
Coin is an implementation of Open Inventor. Open Inventor is the de facto standard API for retained-mode 3D graphics programming. Open Inventor has a highly extensible design, and has been designed to allow for rapid development of highly interactive 3D graphics applications in the fields of CAD, engineering, scientific computing, simulation, VRML, and visualization.
VMD (Visual Molecular Dynamics) is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. VMD uses OpenGL and OpenGL Programmable Shading Language for high performance rendering of large structures.
aiSee reads a textual, easy-to-read, and easy-to-learn graph specification and automatically calculates a customizable graph layout. This layout is then displayed, and can be printed or interactively explored. aiSee features 15 basic graph layout algorithms (including force-directed layout), recursive subgraph nesting, fish-eye views, and an animation interface. It has been optimized to handle huge graphs automatically generated by applications (e.g. compilers).
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.
Mage is a 3D vector display program that shows "kinemage" graphics used in both teaching and research, in applications ranging from estuary ecology to X-ray crystallography model quality assessments. It displays the 3D relationships between data in an interactive environment, which facilitates both open-ended exploration and structured presentation. It includes many tools for on-screen measurement, construction, and editing of the display objects, and can write either kinemage output or various types of 2D images.
skyviewer is an OpenGL-based program to display HEALPix-based skymaps, saved in FITS format files. The loaded skymaps can be viewed either on a 3D sphere or as a Mollweide projection. In either case, realtime panning and zooming are supported, along with rotations for the 3D sphere view, assuming you have a strong enough graphics card.