If you know basic 3d modeling with cubes you should be good to go.
You can un-wrap the model to get the texture UV-map which is generally good to use as template.
Pepakura is definitely a good tool for complex paper crafts.
The first software I use is my imagination! :) And when you use your mind's possibilities you can don't use 3D software, some artists there use only Paint! Your best 3D software is your brains!
Then, you can use Paint, Illustrator, Flash, Photoshop, Inkscape, GIMP and more other applications, as NPT's artists do.
And don't forget to use your mathematics and geometry basic skills (shapes, sides of shapes, angles)...