Now lets see, there's blue, red, yellow, brown, green, orange, teal (or is that cyan), and grey. Now there doesn't seem to be much difference on the main map since all the buildings/units are visible against the background or resources, but in the mini-map things could be a little different (assuming the enemy isn't looking at the main map very closely). Blue could be hidden in the water, yellow looks like gold, and grey looks like stone. These colors could either be missed when passed by in the mini-map as just another resource, or could have the opposite effect where your enemy always checks gold/stone piles to see if it just a pile, or really you. These seem like the colors of choice for stealth.
Or would you rather have a color that stands out no matter what the background, so that you can always spot your units. Red, green, and orange seem to display the best on the mini-map with no confusion at to whether that's your unit or just a pile.
Teal happens to have an annoyance factor, since it is mistaken for blue sometimes if not looking closely. Someone could let a teal peon walk by thinking it to be an ally explorer (luckily an ally can't attack another ally if he thought it was the enemy color). So which is it? I know that many people seem to care, since they will switch from the standard assigned colors in the selection screen. Do you go for the stealthy color, the definitive color, try some confusion, or just leave whatever the hell color the game picks for you? - Bearded_Tim