3D Printing
From Wildsong
Creating designs
OpenSCAD
This is what I have been using so far with my Replicator 2. Works great. This is a script driven tool. You describe the shape you want to create using a simple scripting language.
Blender
This is a freehand 3D drawing tool. It's really big, you can make movies with it. Be prepared to spend a year or so learning how to use it.