In watching a few debates and documentaries concerning athiests such as Sam Harris and Richard Dawkins, I've found some of the athiest responses tend to miss the mark.
For example, there's the small clip of Richard Dawkins answering the question "What if you're wrong?" (link here). While he does make a valid point about your religion being a result of whatever culture and country you grew up in, one aspect that rarely seems to be addressed is the conversion experience.
In the christian doctrine, I could argue that it doesn't matter what culture you're brought up in, I've had an experience with Jesus Christ that has changed my life and many others, and thus I know He is real. And His mandate is to preach Christ to all nations.
Some of the debates I've seen argue the existence of God based solely on text in a holy book versus scientific evidence. This perspective bypasses a whole other aspect of religion: an emotional/'spiritual' conversion experience.
For protestant christians especially, their faith is riding on the coat tails of their amazing conversion. You can point out issues with the bible here and there, and also point to evidence in science that seems contrary to the Bible, BUT most christians will always go back to their conversion experience and say, "THIS is why I know God is real. I don't have all the answers for doctrine or science, but I know that when I got saved in Oct 1989, Jesus Christ instantly set me free from drugs and alcohol and restored my marriage." Hundreds of thousands of christians will tell you similar stories.
Telling such a christian that science shows the earth to be billions of years old won't dent their faith in the slightest. It's going to take a lot more than scientific fact to negate their conversion experience. This is a HUGE hurdle to get over if you're trying to cause a christian to doubt God.
Many 'new' atheists make some excellent points, but they are handicapped in the sense that they were never committed believers to begin with. They are unable to attack one of the major walls guarding a christian's faith. One could say that people in all religions experience a dramatic conversion so it's not something special, but that doesn't seem to be true. Most catholics can't seem to point to a specific time in their life and say "This is when Jesus Christ changed my life, made Himself real to me, and set me free from depression (or whatever problem)". Same with Jehovah's Witnesses. For many religious people, they don't have an experience, they just become assimilated into the religion, like the Borg. Those types of people may be more influenced by scientific evidence.
Matt Dillahunty from The Atheist Experience is a 'real' ex-christian which definitely helps his debates, but other than him, most other outspoken atheists seem to have little christian background.