I've seen a bunch of the classics mentioned - Wrinkle in Time, Chronicles of Narnia, Ender's Game - but there are a couple that were overlooked here:
Watership Down, by Richard Adams. Not necessarily sci-fi or fantasy, but it's an amazing book about the journey of a group of rabbits to found a new home. Yes, rabbits. Don't let that fool you. It's a very deep parable about our world and human nature, and a wonderful story in its own right.
His Dark Materials, by Phillip Pullman. Often called "the athiest's Narnia," it's a nice spiritual companion to the works of C. S. Lewis. Very engaging and thoughtful trilogy of books. The first book is The Golden Compass and worth checking out. Don't let the movie fool you - it's nowhere near as powerful as the book, and the ending... well, they left the real ending out, and the real ending is awesome.