Gombinoscope - Make and mix up faces
Blender - Blender is the open source, cross platform suite of tools for 3D creation.
Cinema 4D - Cinema 4D is a 3D modeling, animation, motion graphics and rendering application.
Abrosoft FaceMixer - FaceMixer is designed to create fantastic face composites with multiple images.
Autodesk Maya - Maya is 3D computer animation software with powerful modeling, rendering, simulation, texturing, and animation tools for artists, modelers, and animators.
Face Gen - The easy way to create realistic faces 3D human faces from 1 or 2 photographs or at random.