I found The God Delusion to be incredibly overrated. It's horribly organized, much of the material is uninteresting to people already familiar with standard anti-Christianity slogans, and its main argument for the non-existence of God (The Ultimate Boeing 747), while valid, lacks the punch of Occam's Razor or The Problem of Evil.
If I was going to recommend a book I would recommend Why Won't God Heal Amputees?, which has got to be the most accessible text arguing for the non-existence of God I have ever read. The last two chapters are annoying as hell, though.
If you can fudge the definition of "book", then LessWrong's own collection of religion-themed articles is excellent. Most of them are under the "religion" tag and the "antitheism" tag, but I think "Reason as memetic immune disorder", which lacks either tag, nevertheless makes some great points about religious compartmentalization.
In an Open Thread comment beriukay mentioned that he's reading C.S. Lewis' Mere Christianity. I've been reading it too, for interesting reasons.
In my case it so happened that I started discussing faith with a long-time online friend whose spiritual views I didn't yet know, and he turned out to be a Christian with a high regard for the Bible, who also has an interest in science. As our discussion turned to our readings on spirituality, I acknowledged (I think it was me) that I probably spent more time on books that reinforce my point of view than on books that challenge it, perhaps a case of confirmation bias. (I've been exposed to many poor arguments for Christianity, and dismissed them; but possibly that was largely a function of having started out with that bottom line already written and picking arguments I wouldn't have much trouble refuting.)
In the spirit of experiment we agreed to a "trade" - he would read (thoughtfully and with an open mind) a book of my choosing on reasons to doubt faith, and I'd do the same with a book he chose on Christianity.
So the idea here is to pick a book that's the "best argument from the other side" (as in quote 3 here).
I recommended The God Delusion - I'm not sure if that's the best choice given the above intent, but it's what came to mind on the spot.
Would you make a different choice? If so, what?