NanoEngineer-1
NanoEngineer-1 is an open-source (GPL) 3D multi-scale modeling and simulation program for nano-composites with special support for structural DNA nanotechnology. It features an easy-to-use interactive 3D graphical user interface for designing and modeling large, atomically precise composite systems.

NanoHive-1
NanoHive-1 is a modular simulator used for modeling the physical world at a nanometer scale. The intended purpose of the simulator is to act as a tool for the study, experimentation, and development of productive nanosystems. NanoHive-1 is a GPL/LGPL licensed open-source development

NanoCAD A freeware nanotech design system including JAVA source code.

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OpenChem project to put together a much more complete and functional program for designing and tinkering with molecular machines.

Molecular Assembly Sequence Software (MASS)  can be best used to view molecular nanotechnology designs.

nanoTITAN, Inc. nVisualizer and nanoXplorer.

Molecular Visualization Freeware Protein Explorer, Chime and Rasmol.

DisMol a freeware molecule display applet.