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.
The problem with that book is not just that it will activate people's defense mechanisms, as some people have already noted, but that these defense mechanisms will often be, on the whole, a largely correct reaction. Significant parts of that book are nothing but ideological propaganda that attacks some metaphysical systems in favor of others, and when people get a visceral reaction that they're being propagandized and not enlightened by the writer, it's a correct intuition, even if it proceeds from spontaneous mental heuristics and not a rigorous logical analysis.
Even setting aside the issue that Dawkins is selling his own metaphysics in an underhanded way, as writers in this genre typically do, many of his arguments are full of errors of both logic and fact that clearly betray his ideological biases. (This is especially cringe-inducing when he takes a superficial and caricatured knowledge of history and colors it with his ideological preconceptions.)
(For full disclosure, I haven't read all of that book, but even if the remainder is much better, what I saw is enough to draw the above conclusions.)
Because of these considerations I'd suggest Pinker's "Blank Slate" - it does undermine religion, but in a much subtler way. It's well argued and less (but not entirely un-) political.
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?