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.
open3mod - A free, Open-Source 3D Viewer designed to make it all easier. Massive 3D Format support
UCSF Chimera - UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular...
cmftStudio - GUI counterpart of cmft - cross-platform open-source cubemap filtering tool.
Jmol - Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry...