Blender - Blender is the open source, cross platform suite of tools for 3D creation.
Avogadro - Avogadro is a free, fantastically easy to use molecule editor.
SelfCAD - SelfCAD is an online 3D modeling and slicing software.
UCSF Chimera - UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular...
SketchUp - 3D for Everyone
Jmol - Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry...