This stage is the most time-consuming and for some the most boring. I create another layer below the inks and name it "flats". Then I begin laying down colors based on the lighting I anticipate from the shot. In this piece, I'm going for a somewhat hellish warground look. The colors are slightly muted, earthy type colors. It's never good to oversaturate colors as the look is often too strong and too difficult to fix. The ink layer is always DUPLICATED above the flats, so I have two ink layers to strengthen the lines. Notice also that I don't go around the bots with darker lines around the edges. This looks good for comics, but I'm going for a high production cel-shaded look found in anime feature films, so the lines need to be uniform. Also, it's really important to start by choosing your light source. It actually affects the tone of colors for me, as well.
There's another thing that I often do before this, shading the shadows, which I plan on showing in the next stage. I think you guys will like this technique as it helped me out tremendously in speeding up coloring, not to mention it really allows you to add more of an artistic flair to your shadows. I used to just pick the polygonal lasso tool and lay down shadows bit by bit, but this was time-consuming and oftentimes the results were not the best they could be. More on this later. Anyways, here ya go: