What's often dubbed "the new atheism" by journalists is a godsend (pun intended) to educated theists. The attacks of men such as Richard Dawkins, Daniel Dennett, Sam Harris, Christopher Hitchens, and their followers on "religion" (a term which, conveniently, covers everything from witch-doctoring to Thomism) contain no new arguments, and their frank, often ill-mannered hostility enables us to appear urbane and judicious by comparison. But most people outside academia, or within it for that matter, don't have time for a point-by-point rebuttal. If you're an educated believer who moves in circles influenced by the new atheism, it's best to have just a few quality resources on hand for dealing with them.
I'm inclined to agree with
Maverick Philosoper Bill Vallicella that the following essays are as good as any for the purpose:
Michael Novak,
Lonely Atheists of the Global Village.
Alvin Plantinga,
The Dawkins Confusion: Naturalism Ad Absurdum.
Alvin Plantinga,
Darwin, Mind, and MeaningRead and absorb those, and you'll have invested all the time you need in acquiring your arsenal.