PubChemSR
PubChemSR is a MS-Windows-based data search and retrieval tool for the NCBI's public chemical database PubChem (PubChem Compound, PubChem Substance, and PubChem Bioassay).
http://cheminfo.informatics.indiana.edu/PubChemSR/

PyMOL
PyMOL is a molecular viewer developed in the spirit of RasMol and OpenRasMol and intended for visualization of 3D chemical structures including X-ray crystal structures of: proteins, nucleic acids (DNA, RNA, & tRNA), and carbohydrates, as well as small molecule structures of drug leads, inhibitors, metabolites, sugars, nucleoside phosphates, and other ligands including inorganic salts and solvent molecules.
http://www.pymol.org/

RasMol
RasMol is an excellent and free molecular viewer available for Windows, Macintosh and UNIX platforms. RasMol is a program that allows you to view molecular structures on the computer screen, and to manipulate them.
http://www.openrasmol.org

SmiLib
SmiLib is a free, platform indepentend software tool for rapid combinatorial library enumeration in the flexible and portable SMILES notation. SmiLib enumerates combinatorial libraries at rates of approximately 9,000,000 molecules per second on fast computers.
http://gecco.org.chemie.uni-frankfurt.de/smilib/

Spekwin32
One of this software's main goals is the consistent display of spectra coming from different sources. At the moment, 13 different spectral file types from commercially available spectrometer systems can be read. Spekwin32 is able to handle UV/VIS, fluorescence, NIR, IR and Raman spectra while the main focus is on UV/VIS and fluorescence.
http://www.effemm2.de/spekwin/index_en.html

Virtual Computational Chemistry Laboratory
On this site you will find tools, which we hope you will find helpful in performing computational chemistry, ADMET and chemoinformatics tasks including the building and visualisation of chemical structures, the calculation of molecular properties and the analysis of relationships between chemical structure and properties.
http://www.vcclab.org