Note: Please recommend other titles in the comments!
I decided to make a list that was a sort of refreshing alternative to the recent bestsellers. I have several reasons for this. First of all, Harris, Dawkins, Hitchens and Pullman are getting so much media attention that you don’t need me to tell you about them. I worry that other magnificent authors are suffering from something akin to the Harry Potter eclipsing phenomenon. Secondly, I wanted to compile a list that wouldn’t chase away closet doubters and struggling theists. I’m not one for preaching to the choir–they’re already converted. These are books that have the potential to provide comfort and challenge to theists and skeptics alike. Finally, I wanted to collect in one place some of the works that were influential in my own upward spiral into skepticism.
1. Rational Mysticism: Spirituality Meets Science in the Search for Enlightenment

John Horgan was a senior writer for Scientific American, and in this book he embarks on a trip that encompasses everything from his personal experiments with the concoctions of Amazonian shamans to well-funded scientific studies on the brains of meditating monks. Rational Mysticism is a fascinating exploration of altered states, mystical experiences, and the biology of epiphany.
2. Varieties of Unbelief: From Epicurus to Sartre

I read this for a Modern Atheism course I took at UCI–the class had a boisterous mix of believers and skeptics and was the most bloody fun I had in any single college class. It’s essentially a short greatest hits compilation of the writings of skeptical philosophers and writers from Hume to Nietzsche, Voltaire to Schopenhauer. This book breaks their writings in to appetizing bites and makes their writings very accessible to non-philosophers like me. It also provides enough challenging questions to fuel hours of debate with minimal intervention from mediating professors.
3. Doubt: A History: The Great Doubters and Their Legacy of Innovation from Socrates and Jesus to Thomas Jefferson and Emily Dickinson

Jennifer Michael Hecht is one of my heroes for writing this book. She turns standard approaches to the history of thought all topsy-turvy and creates this sweeping narrative of doubt. The cast of characters includes Job, Socrates, Buddha, Jesus, Freud and women like Hypatia, Emily Dickinson and Margaret Sanger.
4. Jesus: A Revolutionary Biography

Some of the greatest skeptics are firmly ensconced in their religions, and J. D. Crossan is as Irish and Catholic as he is ballsy in the his pursuit of the truth. I recommend Jesus: A Revolutionary Biography because I come from a Christian background and this helped me to completely humanize Jesus. There are hundreds of comparable Jesus biographies, as well as brilliant and accessible studies that focus on founders of other faiths, including Mohammed, Buddha, and Moses.
5. Women, Family, and Utopia: Communal Experiments of the Shakers, the Oneida Community, and the Mormons

There are many books that look at religions in comparison with each other. Reading these were often humbling experiences for me, as I learned that my own religion of origin was not as unique in its claims as I thought. Women, Family, and Utopia compares the celibate Shakers, the polygamous Mormons and the strangely structured “free love” community at Oneida in the 19th century. Religion scholars are churning out thousands of such titles each year.
6. My Name Is Asher Lev

This is an incredibly moving story of a brilliant young Hasidic Jewish artist who struggles to follow both the truth of his genius and the truths imposed by his religious community.
7. Why Atheism?

Some of my favorite arguments for atheism are calmly, eloquently and simply presented in this compact tome. My favorite is the explanation of justified belief, using an intelligent young child’s convictions of the reality of Santa Claus.
8. The Best of H. P. Lovecraft: Bloodcurdling Tales of Horror and the Macabre 
Lovecraft does an excellent job of making one feel like an annoying little gnat in a universe populated by giants–including tentacled, many-fanged gnat-catchers. HPL is an excellent antidote for any kind of hubris.
9. Essential Spirituality: The 7 Central Practices to Awaken Heart and Mind

I include this book because of its emphasis on practice over belief. Let’s face it–without the infrastructure of religious society and the reinforcement of religious ritual, it can be difficult to find the discipline to regularly cultivate compassion, emotional serenity, and a clear mind. Walsh strips much of the religious trappings off of many of the best of religion’s meditative practices and ethical teachings and distills them into this handy manual. It’s full of fun stories and anecdotes meant to inspire and elevate (kind of self-helpish, but I like this sort of thing).
10. Cosmos

Last, and most certainly not least, is Cosmos by the late Carl Sagan. Much of the science is a little dated, but that’s the point of half of the book–our cosmologies keep transforming, and what was gospel in one age becomes the myths of the next. What persists, however, is the wonder and awe inspired by the natural world. The canopy of stars–billions and billions of them–is a grand enough cathedral.
So, this is my completely arbitrary and incomplete list. Do you have any you’d like to recommend?