I have tried anaglyph mode in openarena, and i have found 2 problems:
1) In color mode there are no color correction of image. And in result
 red or blue objects are visible only by 1 eye.
2) There are no possibility to change brightness/contrast for single eye.
And this leads to different brightness for eye, besause
of different sensibility in red and cyan colors.
Mostly it's noticiable in grayscale mode.