Here is a good one for general engine knowledge of what really goes on to make the car move.
http://auto.howstuffworks.com/engine.htm
This one is pretty good for a quick introduction to the other systems under the hood of your car, and how they work :
http://auto.howstuffworks.com/engine4.htm
Learn to love HowStuffWorks. It is an awesome site, especially for those of us who just cant live without knowing what's actually hapenning.