You can choose your ink color and width on a "per-object" basis. This is fine for most anime styles, IMO.
Sometimes, though, you may want a line that varies in thickness. Here's one method to get that line:
First, apply Fast Fresnel to all of the surfaces that will need "ink." You must apply Fast Fresnel before Super Cel Shader (ie: Fast Fresnel takes up slot #1, SCS takes up slot #2). In FF's Options panel, turn off all settings except for Diffuse. Make sure the minimum Glancing Angle is 0 degrees, and put a negative number (yup, you can use negative values in Fast Fresnel--ain't life grand?) in the Diffuse's Glancing Level setting. Negative 100% would be fine.
You'll get something like this:
Yes, it looks nasty. But when you slap Super Cel Shader on top of that:
Make sure Zone 1 is set to 0.0/1.0-or-lower with a Paint Brightness of 0.0. That'll be your "inking" zone. Adjust the line thickness by tweaking Fast Fresnel's Diffuse Glancing Level. The above image uses a -200% Glancing Level; here's what happens when I change that -200% value to -100%:
Adding Cel-Look Edges at this point might be a nice touch:
Or you could forget Cel-Look and raise the Paint Brightness of your "inking" zones to 0.3 or 0.4, giving you "colored inks" for a pseudo-Disney look:
Just do whatever looks good to you...
Settings for the last image:
Cel-Look Edges; Particle/Line Size set to Small and Edge Color set to RGB 0 0 0. This will put a 1-pixel width black ink outline around the whole object and around each surface.
For the varied-width "inking":
First shader plug-in applied to each surface is Fast Fresnel. In the FF Options panel the only active setting is the Diffuse, which is set at a Glancing Level of -50% (for a thin line). The Minimum Glancing Angle is set to 0.
Second shader plug-in applied to each surface is Super Cel Shader. The main surfaces are the Hair, Skin, and Clothes. For the Hair:
RGB 128 128 255
Zone 1 0.0/0.1 Paint Brightness 0.0 (for a varied-width "ink line")
Zone 2 0.1/0.4 Paint Brightness 1.0 (for a "shadow" of RGB 128 128 255)
Zone 3 0.4/0.7 Paint Brightness 1.5 (for a brighter "shadow" of RGB 192 192 255)
Zone 4 0.7/inf Paint Brightness 2.0 (for a hair color of pure white.)
For the Skin:
RGB 255 204 187
Zone 1 0.0/0.0 Paint Brightness 0.0
Zone 2 0.0/0.05 Paint Brightness 0.0
Zone 3 0.05/0.7 Paint Brightness 1.0
Zone 4 0.7/inf Paint Brightness 1.2
For the Clothes:
RGB 128 1 255
Zone 1 0.0/0.05 Paint Brightness 0.0
Zone 2 0.05/0.5 Paint Brightness 0.7
Zone 3 0.5/0.9 Paint Brightness 1.0
Zone 4 0.9/inf Paint Brightness 255