Free Software
Chemistry Software
Gabedit: (From the product page) Gabeit is a graphical interface to Gaussian, Molcas and Molpro computational chemistry packages running locally or on a remote server. It includes a 3D molecule editor and viewer. Most major molecular file formats are supported and graphics can be exported in many formats.
JChemPaint: (From the product page) JChemPaint is intended to be complementary to Jmol, a visualisation and analysis tool for 3D molecular structures (see below).
Jmol: (From the product page) Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems.
Graphics Software
Flounder: (From the product page) Flounder Flounder is a quick way to visualize regularly spaced 4D data, i.e., a data set that is a function of x, y, z, and time.
Fung-Calc: (From the product page) Fung-Calc is a free, open source advanced, yet easy to use, graphing calculator for Linux using Qt. It plots several types of 2D and 3D graphs. It combines the use of advanced mathematical features and ease of use all in one package.
FreeMat: (From the product page) Freemat is a free environment for rapid engineering and scientific prototyping and data processing. It is similar to commercial systems such as MATLAB from Mathworks, and IDL from Research Systems, but is Open Source. FreeMat includes several novel features such as a codeless interface to external C/C++/FORTRAN code, parallel/distributed algorithm development (via MPI), and plotting and visualization capabilities. FreeMat is available under an MIT-type license. Supported platforms include Linux, Windows and Mac OS X.
Kpl: (From the product page) Kpl is a program for the KDE project (K Desktop Environment). Its purpose is the two- and three-dimensional graphical presentation of data sets and functions.
PLplot: (From the product page) PLplot is a library of functions that are useful for making scientific plots. PLplot can be used from within compiled languages such as C, C++, FORTRAN and Java, and interactively from interpreted languages such as Octave, Python, Perl and Tcl.
Text Processing Software
Latex Equation Editor (Linux): (From the product page) This is a simple clone of the excellent LaTeX equation editor (see below) you can find on MacOS X. There's a zone to type LaTeX input, and it generates an image to represent it (color, font, and size are customisable). You can drag the image to other applications (like OpenOffice Impress, Mozilla, the Gimp). It also exports to any image format ImageMagick supports. It is free as in speech, and is released under the GPL.
TeX on Mac OS X: (From the product page) TeX is a typesetting language. Instead of visually formatting your text, you type your text combined with commands in a plain text file. That file is your TeX source. You then use TeX to produce the final layout. Contrary to a normal word processor, the source and the output are basically separated in two different files.
Tex Equation Editor (Mac OS X): This is a Tex equation editor to use with the TeX on Mac OS X product listed above.
Programming Software
Chemistry Development Kit: The Chemistry Development Kit (CDK) is a Java library for bio- and chemoInformatics and computational chemistry.
HDF5: HDF5 is a general purpose library and file format for storing scientific data. HDF5 is developed at the National Center for Supercomputing Applications (NCSA).
H5UTILS: H5UTILS is a set of utilities for visualization and conversion of scientific data in the free, portable HDF5 format.
ImLib3D: (From the product page) ImLib3D is an open source C++ library for 3D (volumetric) image processing. Focus has been put on simplicity for the developer. It contains most basic image processing algorithms, and some more sophisticated ones. It comes with an optional viewer that features multiplanar views, animations, vector field views and 3D (OpenGL) multiplanar. All image processing operators can be interactively called from the viewer as well as from the UNIX command-line. ImLib3D's goal is to provide a standard and easy to use platform for volumetric image processing research. ImLib3D has been carefully designed, using modern, standards conforming C++. It intensively uses the Standard C++ Library, including strings, containers, and iterators.