I've played with various colors of LED in the dark. The light level has to be very low and make everything appear to be grey. If you can see any color at all, of objects or the LED's beam, your dark adaption is gone.
A bright red LED will ruin dark adaption just as well as a blue or white one. As it is, I run white LED's in my A2 (don't have a M900 yet), to render colors correctly.
Human eyes are less sensitive to red, so the red LED's will appear dimmer than white, and blue will appear brightest. I hear that blue throws the red-brown of blood into contrast and some EMT's use it to spot blood easier. I've never tried it.
Importantly, though, some people can't "stomach" certain colors of light. I like blue better than red. Some like yellow, or green, or blue-green.
I guess all of this changes though if NVGs are involved.
I agree with Hokie: the best point is that whatever color, the LED's are dimmer than the main lamp, save battery life, and lamp life.
If you want flashing red and blue, mount a Ergolight Rav'N to the rail:
http://www.techass.com/el/raven2/raven2.php
;)