The program is Paint, that is all! ^_^
Too make colouring easier, click on the Colour Picker tool. Pick a colour off one Pokemon and LEFT CLICK IT. This is the colour we're going to replace. Next, pick a colour you want to replace the Primary colour using the Colour Picker or your paint pallet. Either way, RIGHT CLICK IT.
With that done, click the eraser tool and hold the RIGHT MOUSE BUTTON. Nothing will happen until you scroll over the Primary selected colour. When you do, it'll get replaced by the Secondary selected colour
USEFUL TRICK: If you have a Primary selected colour, but your Secondary is white and you hold the RIGHT mouse button using the eraser, it will only erase that colour.
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Mudkips are cool. :3 
