pymol - PyMOL is a powerful and comprehensive molecular visualization product for rendering and animating...
Blender - Blender is the open source, cross platform suite of tools for 3D creation.
UCSF Chimera - UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular...
FreeCAD - An open-source parametric 3D modeler
Calistry.org - Calistry is an online Chemistry Calculator.
meshmixer - meshmixer is an experimental 3D modeling tool for making 3D mashups without too much hassle.