I decided that instead of researching this question I would, instead, "Ask The Audience" to give me a final answer for my children. Please vote in the poll below:
1) Clouds are different colors dependent on the color of their mother and father clouds.
2) God decides whether to make them white, black or something in-between so that they match their surroundings.
3) Evolution. Clouds that are best adapted to their environment are most likely to evade their natural predators, and thus are the most likely to procreate. That's why purple, yellow and plaid clouds are relatively rare.
4) Optical thickness, either because of quantity or density of water droplets, prevents light from getting through the cloud.
5) If it's about to rain, the cloud is darker, genius.
