Three novels that changed my life:
Childhood's End, by Arthur C. Clarke - confirmed me in my atheism at age 13. Don't get me wrong, I was already questioning my faith and knew that the platitudes I was being handed didn't wash, but the book reinforced it and crystallized the decision: "there is no God, it's all a fairy tale." I re-read it recently and saw how shallow the book was, but at the time, it put a cap on things.
On the downside, I spent the next 20 years an atheist. On the upside, I rejected the lame/3rd grade version of God most people get, and I had to find my way back by myself. I ended up much stronger for it, although it was a difficult trip.
The Stranger, by Albert Camus. It wasn't so much this story, which I didn't really identify with, but the fact that it led me to other books by Camus, who soon became my favorite writer and had an enormous impact on the way I saw the world. He was the first guy who felt like a kindred soul, to me. Everyone around me seemed to be just acting out superficial social scripts, but he was talking about what really mattered. He opened me up to the love of nature, women, art, and beauty.
Thus Spake Zarathustra, by Fredrich Nietzsche. I was bowled over by this novel. I remember reading it in a trance. Nietzsche was another writer who was very influential in my early life. He taught me about writing and post-modern philosophy (that was his non-fiction). He showed me what an exciting adventure the life of ideas could be, and how much courage and independence was required. He formed my concept of "greatness," reinforced my atheism, and made me a big old narcissist. I've since "overcome" (Nietzsche joke) all of that.
Non-fiction has been a hundred times more influential in my life than fiction, but those are the novels that came to mind.