Software

Afferent
Tools for tracking the information associated with combinatorial libraries and parallel medicinal chemistry syntheses.
http://www.mdli.com/products/afferent.html

Automatic Organic Chemical Reactions
A program based on a mathematical representation of organic synthesis that generates all products of a synthesis on an input of organic compounds.
http://www.aocr.ch/index.html

Building the Shortest Synthesis Route
This article, published in CHEMTECH in 1998, is a nice introduction to the field of Computer-Assisted Organic Synthesis.
http://pubs.acs.org/hotartcl/chemtech/98/sep/buil.html

CAChe Group
Provides software to view and predict 3D molecular structure and properties and to analyze the relationship between structure and properties or structure and reactivity. CAChe is a tool for medicinal, polymer, process and synthetic chemists.
http://www.cachesoftware.com/

ChemNomParse Project
An open source project to create an IUPAC nomenclature parser.
http://chemnomparse.sourceforge.net/

Organic Synthesis Exploration Tool
Free software for computer-assisted organic synthesis, intended mainly for use in education. Applet-based. Source code available.
http://ivan.tubert.org/caos/

SynGen
A program for automatic synthesis generation which focuses on the shortest, most economical routes. Uses a generalized model of organic reactions and functionality to simplify the problem space. Macintosh beta version available for download.
http://syngen2.chem.brandeis.edu/syngen.html

Systematichem
Computational organic chemistry software for retrosynthesis and synthesis development.
http://www.syschem.com

TORVS Research Team
Software for reaction prediction, synthesis design, classification of organic reactions, chemical information, calculation of 3D coordinates, and calculation of physicochemical parameters.
http://www2.chemie.uni-erlangen.de/software/index.html