You may have heard of the very cool and intuitive 3D modeling application Teddy - it's been around for a while. It was developed by Takeo Igarashi, and by now he has developed a more advanced version, called SmoothTeddy (which, alas, does not run on the Mac).
Kokoro reports that there are two console games out that feature this technology.
Kaijuu No Shima (The Island Of Monsters) allows you to create your own monster. This movie, if you are able to watch it, shows how well the monster creation and customization was implemented. It looks like a very nice interface.
Rakugaki Kingdom apparently also allows you to create your own monster, but that's all I know about it.