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The Blue Obelisk Data Repository lists many important chemoinformatics data such as element and isotope properties, atomic radii, etc. including references to original literature. Developers can use this repository to make their software interoperable.
PerlMol is a collection of Perl modules for chemoinformatics and computational chemistry with the philosophy that "simple things should be simple". It should be possible to write one-liners that use this toolkit to do meaningful "molecular munging".
OBExtensions is a extension library for the chemoinformatics library Openbabel.
It provides extensions to Openbabel, being mostly GUI widgets.
OBExtensions has a 2D/3D viewer, 2D coordinates generator and some other extensions.
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