ACD Labs
Advanced Chemistry Development Inc. provides a wide set of desktop and on-line software for chemists and educators: NMR, IR, UV, Mass Spectroscopy, Drawing and Modelling, Chromatography, Naming, Physico-Chemical Properties Calculation, comprehensive databases and predictions.
http://www.acdlabs.com/

CACTVS Chemoinformatics Toolkit
CACTVS is a distributed client/server system for the computation, management, analysis and visualisation of chemical information.
http://www.xemistry.com/academic

CambridgeSoft
CambridgeSoft Corporation is the leading supplier of Internet browser and web server based life science desktop software, enterprise solutions, chemical databases and consulting services to the biotechnology, pharmaceutical, and chemical industries.
http://www.cambridgesoft.com/

ChemAxon
ChemAxon is a software company specializing in providing Java based application programming interfaces and end user applications for cheminformatics and life science research.
http://www.chemaxon.com/

ChemDoodle 3
ChemDoodle is a chemical structure environment with a main focus on 2D graphics and publishing to create media for your structures, reactions and spectra.
http://www.chemdoodle.com/

Chemical Drawing Programs Review
Comparison of chemical drawing programs - ISIS/Draw, ChemDraw, DrawIt (ChemWindow), ChemSketch, Chemistry 4-D Draw, WinPLT, MarvinSketch, etc.
http://dragon.klte.hu/~gundat/rajzprogramok/dprog.html

Chemical Information and Reaction Assistant
CIARA is a program that stores chemical information and assists in planning chemical reactions. It eliminates much of the tedious and time consuming work of calculating data such as molecular weights, moles, reactant amounts, percent yields, etc. A minimum amount of information is entered and CIARA does the rest. CIARA also is a database program so records can be stored and searched.
http://www.vogelscientific.com/ciara.htm

Chemis3D
Chemis3D is a Java Applet which renders virtual 3D molecular models within a Web document. It is specially designed for open interactive molecular visualization on the Internet or via an intranet
http://www.mol3d.com/

Chemissian
Chemissian is a quantum chemistry software to analyze and visualize Gamess/Gaussian outputs - plotting molecular orbital energy level diagrams, CIS/TDDFT-calculated and experimental spectra, electron density/spin maps; compute contributions of atoms and molecular fragments to MOs and draw them directly on the MO diagram.
http://www.chemissian.com/

ChemWriter
ChemWriter is the 2D chemical structure renderer and editor designed for Web applications. Lightweight and feature-rich, ChemWriter is the ideal choice for displaying and creating chemical structures on the Web.
http://metamolecular.com/chemwriter/

Elsevier MDL
Elsevier MDL provides informatics, database, workflow and decision support solutions that accelerate the discovery and development of successful new drugs by improving the speed and quality of scientists' decision making.
http://www.mdl.com/

GIF Creator for Chemical Structures
Computer-generated GIF and PNG images of chemical structures for WWW pages etc. from your 2D or 3D input files. Forms-based interface, automatic generation of 2D display coordinates for structures without them.
http://cactus.nci.nih.gov/services/gifcreator/

GLARE
GLARE is a library and a free software for product based optimization of reagent lists in the context of a chemical combinatorial library design. Large virtual combinatorial libraries containing 10^12 products have been optimized within a second.
http://glare.sourceforge.net

Hyleos: Free Chemistry Software
Free Windows software for working with MDL SDF files and molfiles. Includes descriptors calculation like TPSA, molecular weight, HBd and HBa.
http://www.hyleos.net/index.php

iMol
iMol is a free molecular visualization application for Mac OS X operating system. The program is an indispensable tool for chemists and molecular biologists. iMol allows loading molecules using several file formats: PDB, XYZ, MOL2, HIN, CAR, ALC, BIO. The molecules can be saved as PDB, XYZ or BIO files.
http://www.pirx.com/iMol/