You're probably familiar with Phidias on the DS, pretty neat painting app.
Basically just need a version of Phidias where you have layers, a pencil tool, and can select part of your image, drag it round etc
I did actually pixel a bit in Phidias, you can zoom in nice and close, but since there's no pencil tool, you have to select the brush tool to 1 pixel and hold it down until the colour is solid