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.
Cinema 4D - Cinema 4D is a 3D modeling, animation, motion graphics and rendering application.
ChemDraw - ChemDraw - The Gold Standard for Chemical Structure Drawing and Research Publications.
Autodesk Maya - Maya is 3D computer animation software with powerful modeling, rendering, simulation, texturing, and animation tools for artists, modelers, and animators.
ACD/ChemSketch - ACD/ChemSketch for personal and academic use brings the power of our structure drawing package to your home computer.