Here are five of my favorite books which help me with “Doubting Thomas” syndrome:
The Skeptical Believer by Dan Taylor
http://www.amazon.com/The-Skeptical-Believer-Telling-Stories/dp/0970651155
Proper Confidence by Lesslie Newbigin
http://www.amazon.com/Proper-Confidence-Certainty-Christian-Discipleship/dp/0802808565
Longing to Know by Esther Meek
http://www.amazon.com/Longing-Know-Esther-Lightcap-Meek/dp/1587430606
How (Not) to be Secular by James KA Smith
http://www.amazon.com/How-Not-Be-Secular-Reading/dp/0802867618
Believing Again: Doubt and Faith in a Secular Age by Roger Lundin
http://www.amazon.com/Believing-Again-Doubt-Faith-Secular/dp/0802830773