Sorry to take so long in getting it up. sweatdrop
I also apologize that this does not have step-by-step images to go along. I do have the tutorial in image format, and it can be found at here. You can save it as a one-file reference to follow along. ^^; (Not neccessary, but better for those who work better with visuals)
If there is anything I should change/add/clarify, please let me know. =3

++Requirements:
Computer
Computer graphics program (plus basic knowledge of the program)
Mouse or tablet (touchpad works too, but not very well)
Inked drawing (either traditionally or digitally inked)

++A few notes before beginning:
Any graphics program should work, as long as it supports multiple layers.
Steps may be a bit different for each one, but I've tried to include tips for a few different ones (PS, PSP, OC1.1, Pixia).
PS = Photoshop, PSP = Paint Shop Pro, OC1.1 = OpenCanvas1.1
This image was made in OpenCanvas1.1, and the tutorial was made by screencapping while the event file was playing.
Try to keep lighting in mind throughout the CG.
All coloring goes on separate layers under the lineart layer.
This tutorial was made to be more of a guide than anything else; find your own style and improve through practice. =3

++The tutorial:
1. Open your inked image in your program of choice. If your image was scanned, then you need to clean it first. (You can find cleaning tutorial links in the Art Discussion forum stickies).
Place this on its own layer. In PS and PSP, you'll need to go to layers --> Promote Background first.
In PS, PSP, and OC1.1 the layer mode should be Multiply. In Pixia, layer mode should be Normal.

2. We'll start with the skin here.
First create a new layer underneath the lineart. Layer modes are as follows:
PS, PSP: Normal
Pixia: Hybrid
OC1.1: Multiply
Now select the skin color from the palette/color picker, and choose a tool from the toolbox. Tools are as follows:
PS, PSP: Paintbrush or Airbrush
Pixia: Painbrush/Pen
OC1.1: Paintbrush/Pen or Watercolor
Here, I am using watercolor, but it's really your choice. Always use a soft setting!

Take a large brush and loosley fill in the color. Don't worry about coloring outside the lines.
Now take a slightly smaller brush with a slightly darker color, and fill in the shadows. Keep taking smaller brushes and darker shades until you think the shading is sufficient (I use 3 - 4 shades).
Then take a much lighter color in fill in the light spots. Take the Eraser tool afterwards abd erase anything that's outsde of the lines.

3. Now the eyes.
Still working on the skin layer, take a small brush and color the eye space white. Take a soft grey color and put in a soft shadow along the top of the eye.
Create a new layer on top of the skin layer, but still under the lineart layer. Make this one Multiply mode (exception: Pixia, use Hybrid). Now fill in the base color, add the pupils and shading. You can also add the highlights now, but I'm doing them later.
Erase all color outside of the lines, then merge the eye layer with the skin layer. How to:
PS, PSP: Go to Layer --> Merge Down
Pixia: In the Layers palette, go to Edit --> Merge with Lower
OC1.1: Hide all layers except for the ones you want to merge, then go to Edit --> Combine (Shown Layer)

4. Now the hair. Create another new layer underneath the lineart. Make it the same mode as the skin layer.
First lay in the base color with large brush. Working with a slightly smaller brush, put in roughly where the highlights and shadows will go (use darker and lighter shades of the same color).
Now create a new layer above it, in the same modes as the eye layer was.
Taking a very small brush (1 - 10 px), make many small, curving triangles that follow the flow of the hair. Thing of these as chunks of strands, if that helps.
Take darker shades and smaller brushes and keep going until satisfied (here I used 2 - 3).
Merge the shading layer with the hair.

Now create a new layer in the following modes:
PS, PSP: Soft Light, Dodge, Screen, or Overlay
Pixia: Highlight
OC1.1: Add
Take a small brush and paint in the zigzag/triangle shapes of the highlights (they go wherever there is no shading).
PS, PSP users: You can merge this layer with the hair
Pixia, OC1.1: Don't merge. Pixia crashes/error undoing, and OC1.1 won't let you merge different layer types.

Then erase any color outside of the lines. Usually, I add the eye highlights in white in the hair highlight layer.

5. The clothing.
Same basic steps are used here: New layer in same mode as skin layer, lay in base color, shadows, and highlights.

6. The background.
Again, same steps. Actually, the whole CG consists of the same basic steps. The only difference is the texture, shading, highlight, and painting technique.

7. Now you can add some final touches.
Reflected light: This is rather hard to explain, but if you can notice that objects next to one another will pick up bits of the other's color. You can add this into your CG for extra polish.
Retouching: After taking a small break and looking back, you can fix any mistakes or areas you don't like.
Signature: Don't forget to sign your artwork! X3 You can either do this with paintbrush/pen/airbrush/watercolor tool, or text tool.
Save image: Save a copy in the program's default filetype, so you can save all the layers and such for future editing.
(PS = *.psd, PSP = *.psp or *.pspimage, Pixia = *.pxa, OC1.1 = *.wpb)
You should also save a copy in JPEG or PNG format (after resizing if your image is huge) if you are posting on the web.

++Extra:
OpenCanvas users (any version) can export event files.
OC users who would like to download the event file for the CG I used in his tutorial can go to this PGN page.
many other event files can be found at PGN's user community. =3 PortalGraphics.