Atheism and Naturalism (which I'm currently revising) is a book I highly recommend to other atheists because I wrote it to be the best book on Atheism that there could be, and because I've got nothing but good reviews (just click the link to see for yourself: four good reviews, zero negative). But for those who don't think its appropriate for me to honk my own horn, I've put together a list of good books that I think all atheists should read:
1. Atheism Explained: From Folly to Philosophy (Ideas Explained)
This is a book which is highly readable, covers nearly every argument for the existence of god, and in general is full of good skeptical thinking. More advanced readers in philosophy should try J.L. Mackie's book The Miracle of Theism: Arguments For and Against the Existence of God which is a bit more rigorous but ultimately achieves the same purpose.
2. Sense & Goodness Without God: A Defense of Metaphysical Naturalism
This is Richard Carrier's magnum opus on metaphysical naturalism (the view that nature is all there is, which entails atheism). This book is fascinating, thorough, and includes many facts and arguments which you will seldom see anywhere else. In short, you will learn a lot from reading this book. I don't buy all of Carrier's philosophy, still, he is right much more often than not. This is the best book on Naturalism you can buy. Everything from Ethics to Epistemology to Politics is covered.
3. The God Delusion
Richard Dawkins' book on Atheism and belief. Although Dawkins is a mediocre philosopher and most certainly does not address all of the arguments for God's existence, his centerpiece argument, the Ultimate 747, is valid and is a very good demonstration that god probably does not exist.
4. God: The Failed Hypothesis
This is a book that, more than any other, led me into atheism. It does a remarkable job of debunking the "fine tuning" arguments for god's existence, shows how the universe might have come from nothing, and really prepares you to think critically and scientifically about god's existence.
5. Letters to Doubting Thomas: A Case for the Existence of God
This is a case for theism. But, it is a much, much better defense of theism than I have read or heard anywhere else. It was written by professional philosopher, but he has broken down his arguments so that anyone can understand them. Although I have some misgivings about it, I still think it is a good experience to read such an intelligent defense of theism.
Extra Credit: Books on specific topics related to theism and atheism that I recommend.
Dan Dennett's book on free will and determinism.
The Incredible Shrinking Son of Man
A book by Robert M. Price concerning the historical reliability of the gospels. Presents some very intriguing theories and argues for agnosticism reguarding the historical Jesus because all of the evidence can be plausibly explained from a mythicist standpoint. This is not like any book you've ever read on Jesus!
Why Evolution Is True
An excellent, excellent book on the massive evidence for evolution explained in an easily readable manner.
An Introduction to the Theory of Knowledge (Cambridge Introductions to Philosophy)
This is a great introduction to epistemology (philosophy of knowledge).