What Makes the Aurora Different Colors?
The different colors of the Aurora are a factor of two things: which gas the charged particles are interacting with (oxygen or nitrogen) and how high in the atmosphere the aurora is located. Green auroras, the most common, are caused by the charged particles interacting with oxygen lower in the atmosphere. A picture of this is shown below.
http://www.teelfamily.com/activities/aurora/
Red aurorae are caused by oxygen in the upper atmosphere (usually 150 miles or more above the earth's surface) interacting with these particles.
http://www.athena.ivv.nasa.gov/curric/space/aurora/index.html
Blue aurorae are caused by the charged particles interacting with nitrogen lower in the atmosphere.
http://arcticculture.about.com/culture/arcticculture/gi/dynamic/offsite.htm?site=http%3A%2F%2Fgedds.pfrr.alaska.edu%2Faurora%2Fenglish%2Fintro1.htm
Violet and purple aurorae are caused by the nitrogen higher in the atmosphere interacting with the charged particles form the solar wind.
http://www.northern-lights.no/zope/Contest/Gallery/?lang=en