I think I've got my brain wrapped around this, so let's see if I can communicate it better than Nick... basically, for a cyan/blue anaglyph, you effectively have only *two* channels to work with: grayscale-left and grayscale-right. Thinking in terms of HSV colorspace, the hue (cyan or red) is only relavent in as much as it maps its respective grayscale image onto the correct eye.

As for the respective spectrums of the left and right images, they should be the as close as possible, otherwise the anaglyph will become quite hard on the eyes. To illustrate this, imagine that you are taking a picture of a desert -- red rocks with a blue-sky background -- through a stereo camera, with a cyan filter on the left lense and a red filter on the right. The left lense would see the sky as extremely bright, while the rocks would be nearly black -- meanwhile, the right lense would see the rocks as very bright, while the sky would be nearly black. Put together as an anaglyph, this would be a headache-inducing image to be sure. So, it is best for the spectra to be the same, producing like-toned grayscale images, and broken into cyan and red components later.

Cheers,

Nathan