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.
PLOTICUS is a command line utility for creating bar, line, pie, boxplot, scatterplot, sweep, heatmap, vector, timeline, Venn diagrams, and other types of charts and plots. ploticus is good for automated or just-in-time graph generation. It handles date, time, and categorical data nicely, and has some basic statistical capabilities. It can output to GIF, PNG, SVG, SWF, JPEG, PostScript, EPS, and X11. You can use convenient preset options or create complex scripts with rich and detailed color and style operations.
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.
ImLib3D is a C++ library and visualization system for 3D (volumetric) image processing. It contains most basic image processing algorithms, as well as some more sophisticated ones. Its images are STL-compliant templated containers. It inculdes a viewer that features multiplanar views, interactive image processing, animations, vector field views, and 3D (OpenGL) multiplanar. Its main application is medical image processing.
JMV (The Java Molecular Viewer) is a molecule viewer program/component written in Java and Java3D. It is designed to be an easy-to-use, platform neutral molecular visualization tool which can be used standalone or integrated into a larger program. It provides several molecular representations, multiple coloring styles, lighting controls, and stereoscopic rendering capabilities. It loads PDB files over the web, from the RCSB protein databank, from BioCoRE filesystems, and from local filesystems. The interface can be customized by users, and can be disabled for web-based presentations of molecules to save browser space.
FastVox is an API for volume visualization that can be embedded into OpenGL displays. It features a multi-threaded realtime volume rendering engine which is based on a set of plugins that range from high-speed software-based renderers to hardware-accelerated renderers designed for current generation graphics hardware.
The OpenVL library is a framework for working with 3D volumetric datasets. It provides a standard and uniform API to volumetric data access, storage, and processing. It is designed and built to be fast, extensible, flexible, and easy to use. The library is completely open-sourced and encourages contribution. This library is an ideal choice if you want to write applications that deal with 3D volumes.