JOELib
- Free Java computational chemistry library with support for file conversion, SMARTS substructure search, QSAR descriptor calculation, and process/filter methods for molecular data sets.
- http://joelib.sourceforge.net

Jumbo
- Free kit for processing XML+CML in chemistry. Java 1.4 code, XSLT stylesheets, legacy converters and tools. Also includes tools for generating C++, Python and some F90/5 from the schema.
- http://wwmm.ch.cam.ac.uk/moin/Jumbo4.6

Frowns
- Free chemoinformatics toolkit geared toward rapid development of chemistry related algorithms. Written in Python with a small portion written in C++.
- http://frowns.sourceforge.net/

JChem
- A Java based development tool for building portable chemical information systems.
- http://www.jchem.com

PerlMol
- Free Perl modules for molecular chemistry. Tutorial, reference manual, downloads and mailing list.
- http://www.perlmol.org/

CACTVS System
- A distributed client/server system for the computation, management, analysis and visualization of chemical information of any type. Tool collection for several Unix flavors; some of the tools are distributed freely in precompiled form.
- http://www2.chemie.uni-erlangen.de/software/cactvs/

Open Babel
- Open-source C++ library for molecule file conversion and pattern matching.
- http://openbabel.sourceforge.net/

The Chemistry Development Kit
- Open source Java computational chemistry package which supports chemical structure drawing and the graphical layout of 2D chemical structures.
- http://cdk.sourceforge.net/

Software Development Lohninger
- Software and programming components for Delphi and C++Builder covering mathematics, statistics, scientific graphing, and chemistry.
- http://www.lohninger.com/