BioJava aims to provide a comprehensive set of Java components for the rapid development of applications in Bioinformatics. It contains interfaces for representing Sequences, Features, and other important bioinformatics concepts. It can also read and write sequence data in a variety of common formats and communicate with Ensembl databases and with DAS and BioCorba servers.
ChemApp is a programming tool from the area of computational thermochemistry. It is a library consisting of a rich set of subroutines, based on the thermodynamic phase equilibrium calculation module of ChemSage. It permits the calculation of complex, multicomponent, multiphase chemical equilibria and their associated energy balances. ChemApp is available as object code for a wide range of platforms and as a shared library/DLL. ChemApp "light" is the free version of ChemApp, and although it is restricted in two ways compared to the regular version, it gives you almost the same functionality.
Ghemical is a molecular modelling software package with some nice 3D visualization tools. It supports methods based on both molecular mechanics and quantum mechanics (using MOPAC7, and MPQC for QM). The geometry optimization (for MM and QM) and molecular dynamics (for MM) algorithms are included. Ghemical is written in C++, and hopefully offers a good framework for a generic freeware molecular modelling tool.
Jmol is a Free, Open Source molecule viewer and editor. It is a collaboratively developed visualization and measurement tool for chemical scientists. Jmol is an active project, and there are new features being added to it on a daily basis. Users are encouraged to modify it to fit their needs and to contribute their changes to the project.