Hi Niles,
This is a great question that I answered for someone earlier- different gases give off different colors when they are excited. The different colors in the auroras result from the differnt atoms and molecules in the atmosphere interacting with the energetic particles coming from the sun. For instance, when charged particles collide with oxygen in the atmosphere, a red glow results.... or an collision with a nitrogen atom causes a blue and green glow.
Cheers,
Holly