The following books are extremely helpful in getting up to speed on either the flaws and foibles of Christianity (or religion in general) or the strengths of the scientific method and evolutionary theory. My favorite books are in bold.

Dan Barker
Richard Carrier
Not the Impossible Faith
Why I Am Not a Christian
Proving History
On the Historicity of Jesus
Richard Dawkins
The God Delusion
The Blind Watchmaker
The Greatest Show on Earth
Daniel Dennett
Breaking the Spell
Bart Ehrman
Jesus: Apocalyptic Prophet of the New Millennium
Misquoting Jesus
Jesus, Interrupted
Christopher Hitchens
God Is Not Great
David Hume
An Inquiry Concerning Human Understanding
Dialogues Concerning Natural Religion
Nick Lane
Life Ascending
John Loftus
The Christian Delusion
The End of Christianity
Robert Price
The Empty Tomb
The Incredible Shrinking Son of Man
Carl Sagan
The Demon-Haunted World
Neil Shubin
Your Inner Fish
Victor Stenger
God: The Failed Hypothesis
The Fallacy of Fine Tuning