I'm going to do this based on personal experience. A few years ago I used to color manga scans all the times, for personal purposes mainly, like making sigs and icons as well.
Anyway, I usually use Photoshop CS2 (any of the earlier versions will do too). Since it's a paid program (well, you can always use other methods if you know what I mean) I'd recommend Gimp.
1. First thing I do is finding a workable manga scan, like this one. Then Select a reference picture of the manga, 'but' with colors.
2. Now with the Polygonal Lasso Tool, select each part of the scan, like hair, eyes, clothes, each of them with a different layer.
3. Now color it by using the paint bucket tool.
4. I put my layers in order, like: hair, eyes, clothes and his skin.
5. Now comes the most important part, each layer must be set to Multiply.
6. You can also use the Burn tool to give more deep and a natural feel to whichever scan you'll be working on in the future.
This is all for Photoshop.