Avogadro - Avogadro is a free, fantastically easy to use molecule editor.
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...
ZBrush - ZBrush is a digital sculpting and painting software solution.
Jmol - Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry...
Cinema 4D - Cinema 4D is a 3D modeling, animation, motion graphics and rendering application.