So, I thought I'd post this here...'cause...I feel like it.
Okay, so...this is a tutorial on basically cleaning and coloring line art.
Alright, so, let's start here with a drawing. It's a panel from the cover of my manga.
Things I did before I scanned:
Penciled it out. Inked with India ink. Does this mean you have to use India ink? No, of course not. It's just the media I used. Basically, though, you'll need dark, clean pencil or ink.

So, that's our picture. Kinda dirty, not really clean, yeah.
Now, let's begin!
1. Image>Adjustments>Auto levels (Shift+Ctrl+L).

Little better, no? But we want more!
2. Image>Adjustments>Brightness/Contrast Now, just play around with the brightness and contrast until you get the black and white picture you want, or at least very close.

3. Still have some dirt? At this point, all I can say is: Eraser is our friend. :D However, you probably have a transparent background, so you might want to use the brush tool, color white.
4. Well, we have a pretty black and white picture, now. But we want COLOR! So, here's what we do. First, check Image>Mode, as it might be in greyscale if you didn't already change it. Make sure it's in RGB.
5. Now, the coloring begins! Make a new layer, and put it UNDER the lineart layer.

See? Now, set the Layer Mode of the lineart layer to MULTIPLY.

6. Start coloring on the new layer under the lineart layer. I suggest a new layer for each color. I normally separate by, "Person A's Hair," "Person B's skin," etc.
7. Now you have all your flats done.

What's that? You want to SHADE and HIGHLIGHT? Well, there's more than one way to skin a cat, you know. You can do what I call soft shading or flat shading. (I'm sure there are actual terms for it, but I'm not versed in art lingo.)
If you want to do soft shading, here we go. Flat shading, skip to 10.
8. First, click on your dodge/burn/sponge tool.

You want "burn." This will allow you to shade. Few pointers: The smaller the brush, the more concentrated it is. If you go from shading with a larger brush and have to switch to small, turn down the exposer.
Now, set your range to "midtones." Take your burn tool, adjust it to the size you need, and depending on how dark you want your shading to be (higher the exposer, darker the shading) adjust your exposer. Now, take it and just swipe it over the areas you want shaded (make sure you've selected the colored layer you want to shade). It should come out fairly nice.

(quick shading job)
9. Now, use your dodge tool to do highlights the same way you used the burn to shade. Range needs to be on midtones. Just experiment to get results you like.

And you're done~!
10. Flat Shading. Okay, you have your flats. Now, just take a darker shade of the flat color and simply color in the shaded areas. I use a medium shade (for normal shading) and a dark shade (for those darker areas).

11. Now, take a lighter color and color in your highlights.

And you're done~!
Pros to Soft shading/highlighting:
1. Quicker
2. Easier for those who haven't shaded much
3. You don't have to figure out what color shading looks best
4. Looks more realistic
Cons to soft shading/highlighting:
1. Harder to fix if you mess up
2. Takes time to learn the tools
3. Not much control over the smaller little nooks and crannies of a drawing.
Pros to flat shading/highlighting:
1. Complete control over color and pixels shaded.
2. Looks more anime-ish
3. Easy to fix mistakes
Cons to flat shading/highlighting:
1. You have to have a higher level of knowledge about highlight and shading (what colors work, where exactly to shade, etc.)
2. Takes longer
3. Harder for those that don't work with a mouse well.
I hope that wasn't too confusing. ^^;;
Extra tips~!
1. Find that your white parts are okay, but your lines just aren't dark enough? This might help!
Select the
burn tool, make sure exposure is 100%, and set the range to
shadows. Now, just color over your picture. The lines should get darker while leaving the white part just the way it is--white~!
example:
(compare to the very first picture)

2. Okay, your problem is the exact opposite! Your white parts are kinda ucky, still, but your lines are good. Simple enough!
Select the
dodge tool, keep exposure at 100%, and set the range to
highlights. Just color over the picture, and your "white" parts should now be what they are supposed to be~!
example:
(compare to the very first picture)

Both put together:

So, technically, you could use this method for black and white drawings, I just prefer the other way and use this for drawings that are going to stay black and white or as a last resort. It's up to you what you want to do.
Notes:
Range - If it's set to "highlights," your tool will target the lighter regions of the drawing (white, yellow, etc.) making them darker (if using the burn tool) or lighter (if using dodge.) If set to midtones, it will target the medium colors of the drawing (slightly darker yellows, peaches, reds, blues, etc.) If set to shadows, it will target the darker colors of the drawing (even darker yellows, deep reds, dark blues, browns, etc.)