First thing's first. You need the latest version of Q3Map2, which can be downloaded from http://www.shaderlab.com. If you're using a recent version of GTKRadiant, I think the version of Q3Map2 that comes with it is up to date enough. I currently use 1.2.13, and it works fine. You do, however, need the correct shader, which is included in the Test Map's PK3 file. Just open it up, and put the cel.shader file in your base/shaders folder (baseq3/scripts for all you q3a users...) Also, add the word "cel" to the end of your shaderlist.txt file, in the base/shaders directory. Now you should be ready!

Run GTKRadiant, and build a simple room. I built mine 640 x 640 x 320, I think...but it makes no difference, as long as the player can fit! 

Create whatever geometry you wish in the room. Make sure you build it all out of caulk to begin with. The caulk texture is under tools/_caulk (for SOF2). Cel shading relies o­n geometry to create an interesting play area, so make sure there's lots of neat brushes all around the map. Add a lot of Raised Surfaces, layer the depth of the geometry. Here's an example of what I mean. To make the stairs, I brought the middle down about 4 units, which brings out the ink lines, forcing the cel shading effect. Also, o­n the landings going up the stairs, I added a 4-unit-high brush with an odd shape, just to create more ink line. This adds a bit of interest to the brushes. Here's a screenshot of my caulked room. Don't worry, we'll texture it next.. 

In Photoshop, or whatever your favorite image editor is, create a bunch of small, square images of varying color. Use common sense, and don't do anything too bright. I keep mine kind of pastel, or desaturated. If it looks good for you, though, use whatever colors you'd like. I did mine 64x64, for no reason in particular. The images will be tiny, just flat colors. Don't do anything "photorealistic", or too "textury". You are emulating the cartoony look, so keep it simple. When you do textures for doors, computers, etc....keep that simple too. Here's some screenshots. First is my photoshop files, which you can find in the PK3 in the textures folder. Just very simple flat colors *very important*!   The next image is of a texture I created for a door, in another cel shaded level. You can see how simple it is, but in game it looks great! Consistent style is the key! 

Next, we texture all the visible faces with our flat colors, or flat-looking textures. You can try to emulate the shadows, or just go nuts, like I did. This was put together rather quickly, but it still looks pretty cool. You really can't go wrong, just use your instincts. Leave the faces that you don't see "Caulked". This is advice straight from the guy who wrote the compiler, so I suggest you follow it! Here's a shot of the Texturing in GTKRadiant.  

Add lights to the scene now. I used white light, but you can experiment with whatever color you want. Here's a shot of the lights I put in the scene, but light it however you'd like!  

The last step is to open up the worldspawn entity (with nothing selected, hit "n". This should be the worldspawn). Add the key "_celshader", with value "cel/ink". 

You're finished, and ready to compile! I used the "final" setting in the bsp menu, the o­ne with the "bounce 8" tag in it. This gives the best lighting, though the compile takes a big longer than without it. It's up to you, experiment! Load it up in SOF2, and see how it turned out! Here's a shot of my test level! 

It has been suggested to me, to compile with the -external tag in the lighting stage. This gives it a more cartoony look, by eliminating the lightmaps, creating a brighter world. Try it out for yourself. I prefer the shadows in my cel shading (like Space Jam, or something), but to each his own! Thanks to MastahUK for the suggestion.