Ok, let's see if I can hit everything in one go...here are descriptions of the different shaders and the textures they use.
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Segment Shaders (walls and floors):
lightmap : from FPSC
mytexture_D : the diffuse texture
mytexture_I : the specular texture, specularity is calculated from player eye position (like the default lighting in most 3d apps). Specularity attenuates (fades) as player gets further from segment so highlights do not become overwhelming.
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Static entities
lightmap : From FPSC
mytexture_D : diffuse texture, alpha controls transparency
mytexture_I : specular texture, same as segment shader. Alpha controls illumination. For flickering light shader, divide alpha channel horizontally and place two light states here (on and off). The shader will divide the UV coordinates in the alpha channel, and use a sine wave function to oscillate between the two states for the flickering effect.
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Dynamic entities For dynamic entities, diffuse and specular lighting is pulled from the nearest light you place in your level. Not just intensity but direction as well, very neat! Uses Valve's "Half-Lambert" lighting algorithm. Very forgiving lighting model.
mytexture_D : diffuse texture, alpha controls transparency
mytexture_I : specular texture, alpha controls cubemap reflectivity
mytexture_N : normal map (I may use the alpha here for illumination if the entity needs self-illumination)
mytexture_S : cubemap
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Water effects
Waterfalls: uses a scrolling UV shader combined with normal, specular, and cubemap. Almost no diffuse component here. The look of water is made almost entirely of reflections of light and environment.
Puddles: Use a "UV-walking" shader. Like a sprite on steroids

Number of frames and framerate is user specifiable in the shader. Uses normal, specular, and cubemap textures.
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These are the "meat and potatoes" shaders that give it the overall look. There are variants on these shaders included for subtle varations. As well as some more "spot" effects yet to be shown (movie screen, animated light shafts, television effects).
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"bond1 - You see this name, you think dirty."