First, you need to start off with a sketch~! But if you already have a scanned in lineart, ignore this and skip to step 3.
Here's my sketch, ignore the ugly monchhichi looking thing.. well at least I TRIED to draw monchhichi, blah~
2.) Lineart
Now here, I just inked over my sketch on a new layer~ I did the glasses in a different layer using a different color. o.O A lot of the time, I do this for everything, skin, hair, clothing etc. I do that to give the image more volume as thick dark lines flatten an image. Yes, I learned that in my illustration class. X3 But for this, I'm going a different route.
3.) Polished Lineart
Ok, I flattened my lineart, (Layer>>flatten image.) excluding the layer with the glasses. I colored my lineart by going to Image>>Adjust>> Hue/Saturation.
When the popup shows up, check off colorize square. Then just adjust the hue to whatever color you want your lineart to be. Also adjust the lightness. Make it light enough so that it's still dark, but you can see some color.
Now duplicate the lineart, and change the duplicate layer to "Screen". Just drag lineart to this icon 
in the layer window to duplicate layer. Change the opacity of the duplicate lineart to about %35-%50 or whatever looks to your eye. Then flatten layer.
*note, you can always polish lineart however you want. Some people just want to leave it as it is, and just adjust brightness and contrast and some people blur their duplicate lineart first, then change it to a different layer mode (overlay, screen, soft light, etc). So feel free to experiment.
Now make your lineart a "Muliple" layer. So that the white area will transparent and you can color under the lineart. See Image Below
4.) Base Color
Now were coloring! It's easier to color everything when you fill the areas in with a base color first. So start filling in a base color for everything, like what you see in my example. Preferably you should make a layer for each area. See my layers window. This makes coloring easier and it's more organized.
5.) Shading
For each layer, make sure to check off "lock". This lets you color inside a colored area and only the colored area. For tablet users, grab the free form pen tool.
For mouse users, you can either use the regular pentool if you know how to use it, or use the polygon lasso tool.
For Mouse users, it's just simply click and drag. Then close path when you've reached the starting point (you'll see a small circle. This indicates the path will close). Then fill the area with a darker shade of the color of your area.
Pen users.
When selecting an area to shade, you need to draw your path first. So draw your path. See images below to see how a path should look and how to turn it into a selection.
After you've drawn your path, right click and click make selection >> ok
A great thing about the pentool method is that you can make more than one path and turn it into a selection. But in order to turn all the paths into selection areas, you HAVE to close all the paths. Which is basically the same with a lasso. You will see a small circle, which indicates it will close the path. See the two figures below.
Once you have the paths all closed, right click and make path into a selection. Then fill the area with color.
So this is where you should be at now. Your image should have some shading~! =D
More shading~! To give more depth to your picture, you're gonna layer on another set of shades over the current shades. See image below.
Now repeat and layer on more shades.
7.) Highlighting
AS you can see, I have added more shading, and added highlights. See image below..
Like the shading, continue to layer on the highlights.
When you're finished, you will get something like this:
This method works really well with hair, the more you layer on the highlights, the shinier the hair will be~ Don't overdo it on the clothing unless you want really shiny glossy clothes. (o.O Sassy~! )
8.) Eyes
For the eyes, you basically use the same layering method of shades and highlights. You want the top to be shades and the bottom part of the iris to be highlights. In my picture, you won't really see it much, since I did most of the shading when I did the inking. I usually keep the eyes empty and shade with color.
9.) Color atmosphere shading
Oo, is your picture in a dark setting? And you want to add in shading that will match the objects surrounding? It's easy~! It's basically using the layering method again, except you're using a different color. For my image, the dominating color is purple. So added in some purple shading on the subject.
From here, just paint in, or color in your background. =D
10.) Color atmosphere highlighting.
Since there are now bright purple lights in the back, it makes sense to add some highlights. (*Note I'm not accurate on shading and highlight. So don't bite my head off for this. =p Besides, if you know better, why are you looking?! lol). So I took a bright tint of purple and highlight areas which I thought the light would reflect off of.
Ok, your picture might not have a person wearing glasses, but you can at least see how I do it. See image below.
Here is my glasses layer~ X3 It's on top of all my layers.
Make a layer under the glasses lineart layer and fill a base color.
I lowered the opacity of the base color layer so that it's transparent and you can see some of the color of the eyes. The picture on the right shows where to change opacity for those who don't know where~ Lower the opacity as much as you want, depending on how transparent you want it to be.
Make a new layer on top of the base layer. And make a selection to shade the bottom areas of the glasses. Like the picture above. Lower the opacity of this layer as well. Just enough to see alittle transparency, but still see it as a shade.
Make a new layer over the shade layer, but this time make highlights. Lower opacity, then repeat this step again to make extra highlights, like what you see in the image above. I did 3 layers of highlights. You can see them in the image. I have the first layer of highlight, then I layered it with smaller shapes on a 2nd layer. The diagonal highlight shape was on the 3rd layer, but instead of lowering opacity, I changed the layer to "Overlay"
12.) Atmosphere Effect
Now to tie your image together, I like to do what I call the "atmosphere" effect. (whatever XD) Basically I use this method to cheat. For example, instead of shading a night scene from scratch, I do this to help me make it seem like the image is dark. This is probably confusing you. Just look at images below. =p
At the very top (above all layers), make a layer. And fill it with a gradient. Since my scene is very purple, I did a purple gradient.
Now make the gradient layer an "overlay" layer. And lower the opacity to as much as you want. Depending how intense you want the color to be. Sometimes the gradient will look bad, so you may have to experiment with gradient color choices.
You can't see a huge diffence here, because I had the gradient layer opacity very low. But if you look at the pants, you'll see a slight difference. This effect will vary on image to image. Sometimes it will work, sometimes it won't.
13.) Soft look
You may have seen some CGs with a very soft look to it. This is how I do it~
Flatten your image, (copy 1). Now duplicate your picture (copy 2). Make sure you're on copy 1. Now go to Filter>>blur>> Gaussian blur.
I can't tell you how much to blur it, since gaussian varies depending on how big or small your image is. See the image below to see how blurry it should look.
Now go to Copy 2. Lower the opacity of that layer to about 75% or to however soft you want your image to look. See the image below for the before and after.
See how soft that looks? =D Isn't it pretty??
14.) Finish~!
After that, you should have a finish product~! Feel free to add any finishing touches yourself~ ^^ Click on the image to see bigger version~
Here is the same picture but different background. =p I did this after I finished taking screens. I hated the other background. XD Instead of trying to do something lame and scenic.. kinda, I just did a graphic background. Just a combination of circles and lines.
You may have seen some CGs with a very soft look to it. This is how I do it~
Flatten your image, (copy 1). Now duplicate your picture (copy 2). Make sure you're on copy 1. Now go to Filter>>blur>> Gaussian blur.
I can't tell you how much to blur it, since gaussian varies depending on how big or small your image is. See the image below to see how blurry it should look.
Now go to Copy 2. Lower the opacity of that layer to about 75% or to however soft you want your image to look. See the image below for the before and after.
See how soft that looks? =D Isn't it pretty??
14.) Finish~!
After that, you should have a finish product~! Feel free to add any finishing touches yourself~ ^^ Click on the image to see bigger version~
Here is the same picture but different background. =p I did this after I finished taking screens. I hated the other background. XD Instead of trying to do something lame and scenic.. kinda, I just did a graphic background. Just a combination of circles and lines.
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