I am often asked the question "What tools can I have my students use to construct images and content in stereo 3D?" There are many options, but here is my short list. Feel free to post a comment highlighting other tools not listed.
Unity offers a free version for educators. Used in heavily in North Carolina schools unity3d.com
Blender is a free open-source tool for educators. Used in heavily in Iowa and VREP schools http://www.blender.org/download/get-blender/
Reallusion offers iClone V, a low-cost design tool reallusion.com
Houdini offers a free apprentice/educator version of this tool used to make most Hollywood movies! http://www.sidefx.com/index.php?option=com_download&Itemid=208&task=apprentice
Maya (just google maya stereoscopic 3d for more resources; the word stereoscopic is important) http://usa.autodesk.com/maya/
Eon Reality offers Eon Creator, a commercial tool
Sculptris is a tool some of the schools in the VREP program are using to great effect. http://pixologic.com/sculptris/