Gombinoscope - Make and mix up faces
Blender - Blender is the open source, cross platform suite of tools for 3D creation.
Sculptris - Sculptris: Enter a world of digital art without barriers.
Abrosoft FaceMixer - FaceMixer is designed to create fantastic face composites with multiple images.
Misfit Model 3D - Misfit Model 3D is a 3D model editor that basically operates with triangle-based models.
Face Gen - The easy way to create realistic faces 3D human faces from 1 or 2 photographs or at random.