Not sure what you mean with designed for model making.
I use the free open source software
Blender
to create the 3D models. If you want to start learning you might want to wait a little as a major update is about to be released which will be much easier or rather intuitive to use. There also is an add-on which will allow you to cut and unfold the model as needed.
Other good 3D software to start would be Sketchup (also has an unfold add-in) and I hear a lot of good things about Tinkercad (although I haven't used that one).
For painting and layout I use Gimp and Illustrator. I think you can also layout with the free open source software Inkscape.
If you know of other software specifically designed for paper model making (other than pepakura) I would be very keen to learn what exists!
Chris