MOLDA - Molecular Modeling and Graphics System using VRML Viewer :: Download Source Code
MOLDA is a molecular-model building program (valid molecule file formats are MODRAST/MOLDA and MSC's XMol XYZ file format). Threedimensional(3D) molecular structures in VRML format can be generated from a variety of molecular science programs (such as MM2,Gaussian94 and Amber4) using MOLDA. Related java and perl programs are also available.
http://cssj.chem.sci.hiroshima-u.ac.jp/molda/

Stirling Engine Animation :: Download Source Code
The site Stirling Engine Animation shall illustrate the functioning of an Stirling engine. The phases of a Stirling cycle are displayed in a left window as animation for a simplified engine. Another window shows the corresponding P-V diagram.A buttonbar is used to control the animation (the speed, start, stop,..). Background information about the functioning of Stirling engines and links of Stirling engine related sites are included.This application includes Java-Applets and Javascript.
http://techni.tachemie.uni-leipzig.de/~stirling/

NanoCAD :: Download Source Code
NanoCAD is a program for assembling and modeling smallmolecular structures. Over time, it will hopefully evolveinto a useful tool for nanotechnological design.
http://world.std.com/~wware/ncad.html

MoleculeViewer :: Download Source Code
This is a revised and extended version of Sun's Demo from SDK1.0.2 MoleculeViewer. This version also reads and displays PDB formated files besides the XYZ formated files.
http://www.sci.kun.nl/sigma/Persoonlijk/egonw/java/Viewer/