Recently, I have been active in discussions on the web concerning Atheism vs Christianity. I've argued with many atheists over the existence of God and these discussions always end with, "Show me proof that God exists."
It's amazing how atheists love to jump behind the scientific method as the only acceptable epistemological method of learning truths. They jump into this "box" largely to protect their beliefs from attacks from "other" sources of truth such as feelings, philosophy, the arts, and revelation. To them, the scientific method is the "end all" of ways to discover truth. In my opinion, that's awfully convenient for their belief system and horribly restrictive to just observed reality. The scientific method is only as good as our instruments, thus, there remains many unseen truths yet to be discovered, some of which can be discovered through other methods and subjects as aforementioned.
One of the greatest pitfalls for atheists when dealing with Christianity, is that traditional Christianity is fantastically confusing and irrational. Below is an excerpt from an atheist regarding how unreasonable Christianity sounds to him:
"Please explain a three-in-one creator deity that created humans from mudpies and ribcages, then a talking snake in a magic garden told them not to eat an apple but they did eat an apple so that's why there are natural disasters and cancer and childhood deaths and rape and murder, and then the three-in-one deity sent a third of himself down to earth to impregnate a woman with another third of himself, then that third of himself sacrificed himself to another third of himself to spare us all from the wrath of the collective whole. Until you do, I do not have to consider your stance to be rational."
Now, the above statement would be difficult for the average Christian to explain in a rational way, in fact, impossible. The above demonstrates exactly how perverted the original Christian teachings of Jesus Christ have become. The bible has many missing pieces from lost books and letters to translation errors to intentionally removed pieces. If this were not the case, there would not be this confusion concerning Christianity, the biblical accounts would make perfect sense, instead they lead to this confusion which really is impossible to explain in a rational and logical way without divine intervention and interpretation.