This may not fit into most digital artists' workflow (especially for comics), but the one thing that makes base colors fun for me is...choosing them. ^^
I used to just use shading to set the mood, and pull the base colors straight from some pre-determined palette, but I found I started getting better-looking art when I made the base colors part of that process. They became a way to sort of practice and anticipate how I would shade later; they laid the groundwork for the mood and color grading of the scene.
But in general, when I have 'lineart' with a lot of gaps in it, I usually just start by making a base-color blob, like this:
Usually, the lines with the largest number of gaps are the long ones that form the outline of the drawing, so creating an outline of color ahead of time takes care of a lot of potential annoyances.
And after this is done, sometimes you find that you can use the paint bucket to fill in a lot of the inner spaces right away, and there're only a few left that you have to paint in yourself (although with real sketchy lines like this, it's better to just paint everything in, since there are so many 'false outlines'. But you can still use the paint bucket to give yourself a speed boost occasionally, or do some quick masking...in case it isn't obvious, I deal with this a lot). ^^