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...
SelfCAD - SelfCAD is an online 3D modeling and slicing software.
Jmol - Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry...
SketchUp - 3D for Everyone
UCSF Chimera - UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular...