The Chemistry Development Kit (CDK) is a library of Java classes for chemo-, bioinformatics, computational chemistry, and chemometrics. It provides important algorithms like substructure search, SMILES, Gasteiger charges, QSAR descriptor calculation, 3D structure generation, 2D layout and rendering, many IO formats, atom typing, and more.
Convex 3D is a convertor, extractor, and viewer for such popular 3D formats as 3DS, Wavefront OBJ, and Lightwave 3D. It is written in C++ and uses a modular design. The package includes a standalone conversion tool (console) and GUI application (Qt and OpenGL are required) for viewing and more. It is not meant to be a modeler, but it can be a powerful tool to hack into 3D files made by 3rd party modelers.
LiquidMaya is a Maya to Renderman plug-in that handles full Renderman output support with a focus on speed, efficiency, and extensibility. Its features include procedural rib generation, full network rendering support, segmented rib files, a shader assignment interface, and much more. Along with the ability to write full C++ plug-ins, it is incredibly easy to script Liquid with Mel. Liquid was used for the visual effects of the "Lord of the Rings" movie.