Photoshop workflow? Manually filling shapes...

maybe use a smallish brush tool at 100% opacity on a new layer to "re-trace" an object and cover the line art, then fill that shape. Or try the "refine edge" tool which I think only works on a mask. Sounds like it's going to be a bunch of hard work if the original drawings are traditional pencil/or pen vs a digital method like a cintiq.

LittleBlackBird.net

I'm assuming the line art is just black lines on a white background? If so, you could try this:
- Switch the blending mode of the line art layer to Multiply
- Create a new layer for your color fill and place it under the line art layer
- Use the magic wand tool to select an area you want to fill with color
- Go to Select>Modify>Expand and enter a small number like 1 or 2 to expand the selection
- Set the foreground color to the color you want to fill and hit Alt+Backspace (Cmd+Backspace on Mac) to fill the selection with color

You should now have a perfectly clean fill with no fringe because the edge of the color fill is covered by the black line art on top of it. You may have to play with the expansion amount to find the right value for the thickness of the lines. To save more time create a simple action to repeat the selection expansion by making a selection and then opening the Actions Palette (Alt+F9), creating a new action, pressing the record button and expanding the selection by the amount you want and hitting the stop button. Now instead of having to go through the menu every time you can just hit the play button for that action and it will expand the selection. You might even be able to create an action for the whole selection, expansion and fill process, depending on how much each image differs from the next. Just keep in mind that the action records where you click when you select with the wand tool and will repeat it in the same place.

HTH