CACTVS System http://www2.chemie.uni-erlangen.de/software/cactvs/
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.
Frowns http://frowns.sourceforge.net/
Free chemoinformatics toolkit geared toward rapid development of chemistry related algorithms. Written in Python with a small portion written in C++.
JChem http://www.jchem.com
A Java based development tool for building portable chemical information systems.