This video gives you the basics of animation in Photoshop by showing you a simple loading animation. TutCast does a great job of showing you how to make a cool .gif animation, but in fact showing you the basics of animating an image. (I.e. the eyes of a person to answer your question)
http://www.youtube.com/watch?v=xvOcC...eature=related
After watching, you should be able to put different frames together (different colors of eyes for example) and create a simple animation of eye color. (It's .gif format, so I don't know about flash)

Hope this helps!