Hi there!
The different colors seen in the beautiful Auroras are related to the different atmospheric gases that are being excited by the energetic particles at that moment. Since the concentration of those gases (atomic oxygen and atomic/molecular nitrogen) varies in altitude, the color will also indicates the Aurora's height.

You can read more about it here: http://www.aurorasaurus.org/learn#aurora-colors and also join Dr. Liz MacDonald web seminar tomorrow to learn more about Auroras. Keep tuned!