Here's a step-by-step process for one of my coloring techniques! Note that this is a process, not necessarily a tutorial, but I'll try to be as thorough as possible.
First step is to prepare your lineart, making sure to have it on top of every other layer. I do all of my work in Clip Studio Paint EX with a Cintiq 13HD tablet so all of this is being done digitally, but if your lineart is done traditionally you can easily extract your lineart by converting the brightness to opacity.
You then can change the background color by double-clicking the icon on the "Paper" layer and making your selection. I chose a greyish purple as my starter.
Next step is to lay down where you're going to color. While on the lineart layer, select the area outside of the lineart and then select "invert selected area".
Once you've inverted your selection, create a new layer underneath the lineart layer. Select any color you want to lay down as the area where you're going to color (I'm using gray), then use the fill tool or press alt + backspace to fill it in.
So far, your layers should look like this:
Next step is to lock the opacity of the "flats bg" layer by selecting the "lock transparent pixels" icon:
Why this step? This is to establish your coloring area, and it will prevent you from accidentally coloring outside of the lineart. Now, you can choose to color and shade everything on "bg flats", but if you want to be more organized and color everything separately as well as making sure everything stays within the boundaries of flats bg, you can create a new layer above the flats bg layer and then select the "Clip to Layer Below" icon:
Since this was a quick piece I didn't separate all of the colors into different layers, so the flats are all done on one layer. I chose to go with dark colors first instead of coloring then shading because I wanted to try and get a feel of the lighting source. I can't really explain it, but this tutorial here can explain lighting better than I can: http://www.androidarts.com/art_tut.htm
Next step is to add the highlights, paying close attention to the shapes and light source. Since the light source is coming in from the upper right, very little light will appear on the far left.
Now it's time to add in some special effects. To make the colors look like they're "glowing", I copied the flats layer and then used Filter > Blur > Gaussian blur (I don't remember the intensity, so you're going to have toe play around with that yourself). I set the opacity of that layer to 33% so that you can still see the cel-shading below it:
I then made some adjustments with the blurred layer by adding a Layer Mask.
Why? A Layer Mask works differently than a clipped layer, and it's where you can erase certain parts of the layer without affecting the original layer's contents. This saves time and effort and can be used for various other special techniques.
The next special effect I added was for depth. I added a new layer above the blurred layer with a purple-to-transparent gradient set at 52% Linear Burn in order to darken the area below the waist of the Call Box Killer, and then I copied that layer and added the same effect onto the Background/Paper.
The colors are looking a little dull to me, so I decided to add a Level Correction Layer by right-clicking the blurred layer (so that the new layer goes directly on top of it) and selecting New Correction Layer > Level Correction....
This changes the values of the colors, and I decided to make them a little darker to match the lighting. After playing around with the values, this is how it turned out:
And finally, I added a little more color to the piece by using a gradient map layer over everything and setting it to "Overlay" at 100%. I right-clicked the lineart layer, then selected New Correction Layer > Gradient map..... This dialog pops up and then after playing around with several colors I made my gradient selection:
And voila! Now you know how I created this piece.