The red and black quinoas have a nuttier taste IMO.

Flavor differences are subtle but the color can also give eye appeal to your presentation. Recently I stuffed roasted red peppers with black quinoa and a friend who I've turned into a quinoa addict (first one is always free) really liked the flavor combination.

Yea, the lighter colored quinoa hae a more delicate taste and the darker ones seem to be earthier.

Darker color, darker taste: more rich and complex.