No issue has caused me to question my Christian beliefs more than what is often called the problem of evil.  Ever since the Greek philosopher Epicurus (342-271 BCE) first questioned the existence of God due to the existence of evil in the world, people have faced this problem and often walked away from the faith of their childhood.  The reality of suffering in light of the professed goodness and power of God is the catalyst that is most responsible for the shift in my own theological views.  

Links:

A much more thorough look at this issue, with citations - Worth the read if you have the interest!

Process Theology

Charles Hartshorne

Tim Keller, a Christian author, tried to address this issue in his book Reason for God, but it is entirely unsatisfying and insufficient.  Neil Carter explains why in this article.