Blender - Blender is the open source, cross platform suite of tools for 3D creation.
pymol - PyMOL is a powerful and comprehensive molecular visualization product for rendering and animating...
FreeCAD - An open-source parametric 3D modeler
Jmol - Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry...
meshmixer - meshmixer is an experimental 3D modeling tool for making 3D mashups without too much hassle.
UCSF Chimera - UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular...