How to Bake Grease Pencil strokes to a model
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DO NOT BOTHER. THIS IS TEDIOUS COMPARED TO JUST TEXTURE PAINTING.

Having been warned, here you go...

You may not know this, but you can draw on top of a surface of a model 
using Blender's Grease Pencil tool. This is under the "Stroke Placement"
setting in the Grease Pencil tab. You can then convert a Grease Pencil 
stroke to a curve in the same tab. Curves can be converted while in 
Object mode (ALT+c) to a mesh.

Next, you can assign a material to that insane mesh with whatever color
you want and perhaps should make it shadeless. Repeat all of these per
color. When done creating all of your "color objects," join them
together. After joining, you will need to switch to Edit mode with your 
combined "master color" object selected and then extrude (e) everything 
just enough to have some faces thick enough for the Baking; otherwise, 
it is just vertices and edges, which will not transfer material color.
BUT BE WARNED: There will be a LOT of faces when doing this; the 
view-port may lag or Blender may crash.

Finally, assuming that the model you were pseudo-coloring on with the 
Grease Pencil is UV unwrapped, you can go to the render settings and 
Bake the texture of "Selected to Active." Distance: 1; Bias: 0.001. 
This is how you bake Grease Pencil strokes to a model.

"Selected to Active" means selecting the "master color" object first and
then the model underneath you want to bake the color information to.

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Afterthoughts...

Having the above said, you are MUCH better-off using the Texture Paint 
mode's "External" option in the Tools tab set to the same resolution or 
higher as the Diffuse Color slot. However, when the image shows-up in 
the digital art program, make sure to draw on a separate layer and save 
changes with the original layer disabled or removed. Otherwise, it will 
mess-up the base coloring sense the exported image is not 100% exact as 
to what you see in the viewport of Blender, even with "Shadeless" 
enabled.

I recommend using 'GIMP' or 'MyPaint' as your external editors.
Preferences --> File --> Image Editor: [/path/to/GIMP/binary]