--------------------------------SOME EXTRA STUFF NOT MENTIONED ABOVE:
Note - these apply to Paint Tool SAI. If you use Photoshop, I might be able to help you as many of these things do apply with both programs, but otherwise, I apologize. If you want individual settings for SAI tools, or just have some questions, feel free to ask!
I usually use the Pen tool to do line art, the size varying on how clean I want to make it. At the moment, though, I'm experimenting with the Ink Pen tool, and I'm starting to favor that more to make cleaner lineart.
2. Base Colors
Again, I use a combo of the Pen tool and Bucket tool to fill stuff in. The Hue/Saturation setting comes in handy if you want to experiment with possible base colors.
3. Shading (dark colors)
For this, I turn on the "Preserve Opacity" setting on the base color layer and go over shadows with a combo of the Water tool and the Brush tool. I'm a bit of a cross-hatcher, so I keep the Brush tool at a smaller size. Make sure you know where your light source is coming from!
4. Shading (light colors)
Same case as above, though I'm a bit more careful when it comes to highlighting, since I'm pretty much working on this all in one layer. Preserve Opacity is still on, though check to make sure you didn't miss any spots.
5. Effects (overlay)
I abuse this function to no end, heh. Set a new layer to Overlay over your image and start accenting parts like shadows with a different color with the Water tool and Brush tool. I love using purples, blues, and reds on flesh tones since it produces a nice effect, but feel free to try other colors too. Play around with the Hue/Saturation function as well - you might find something you like.
6. Effects (luminosity)
Basically, how to make things shiny, haha. Don't do this too much, but a little white here and there doesn't hurt. Still using the Brush tool, by the way.
7. And now for some other things. (optional)
Change the lineart color. Mess with the hue/saturation after you're done. Add a texture. Lots of possibilities for you to toy around with. (:
As for additional detailing, I usually open a new layer over the whole thing and go over it, disregarding the lineart underneath. In other words, lineart is not my top layer by the end. If you wish to add designs and what not, textures or a simple overlay can help.
And that's about it, really.
Probably missed something somewhere, but that's pretty much how I color. This should not be in any shape or form be taken as a standard though, heh. Use this instead as a way to find your own coloring method. (:
extremely rushed coloring guide was requested by ~BizarroFreak17. I'll probably make a better one in the future, but for now, here's a basic one with simple shapes.
Hope this helps!