Pmx Editor - PMX Editor is for editing 3D model data to be used in MikuMiku Dance.
Blender - Blender is the open source, cross platform suite of tools for 3D creation.
3DTin - 3DTin is a browser based 3D modelling tool.
SketchUp - 3D for Everyone
DeleD CE - DeleD is a 3D modeler and level-editor combined into one.
AC3D - AC3D is a 3D software for games, virtual reality and flight simulation, scientific, medical and general data visualisation, rapid prototypes of 3D designs, 3D printing, Google Earth, X-Plane, Second Life and more.