I've used blender. It's freeware.
http://www.blender.org/
There's quite a bit of a learning curve to it but there's some tuts online that should help. The biggest help, though, is just getting in there and getting your hands dirty. Maybe find a model that you'd like to modify and just play around with it and see if you can do the modifications that you want.
That's what you'd use to make 3D models on a computer. After that, you can load them into Pepakura Designer/Viewer and then print them out and put them together.
