For a good anaglyph you need two things:

1) The two images should be in the same waveband AS EACH OTHER, so that everything is responding in the same way. It doesn't matter if those wavebands are visible or not, or happen to be red or blue, so long as they match.

So, the filter combinations that are the same between L and R pancams are L2-R2 at 750nm (near IR) and L7-R1 at 430 nm (violet).

At a pinch, you can use two dissimilar wavebands, but the 3D effect gets harder to invoke.

The use of blue and red in the anaglyph is a way of splitting the images to your two eyes, using coloured filters.

2) The separation of the lenses should be similar to the separation of the human eyes (6.5 cm / 2.5"). The MER pancam is built with 30 cm separation and an inherent 1 degree of toe-in (cross-eye).

The ~ 5x separation is why relief of near objects is ridiculously enhanced, and the toe-in is why the horizon doesn't match. People have commented that you need to shift the images so that the depth of greatest interest has no shift, and other depths are sacrificed.

If you want to be real smart, you could build-in a variable shift for "near", "midground", and "far" viewing...