In case you haven't seen it yet, you might want to check out the interview/debate between Richard Dawkins and a Mehdi Hasan of Al Jazeera above.
I felt that Dawkins should have done a better job when the interviewer brought up Stalin and Mao Zedong. As I argued here, Stalin's atrocities were made possible because he ruled a state that had inherited a centuries long tradition of absolutism from Russia's tsarist predecessors. The same can be said for Mao Zedong, who became dictator of a country that had been ruled by emperors for millennia.
One could also bring up the millions who died during China's Taiping Rebellion, which was led by a failed aspirant to the civil service who styled himself to be the brother of Jesus Christ.
To me, the whole argument of whether or not religion is a force for good in the world and whether the world would be better without religion is a stupid argument. The way I see it, the world would be a better place if more people would be good regardless of whether they were religious or not, just as the world would be worse off when more people are bad, again regardless of whether they are religious adherents or atheists.
The problem with the communist dictators is that they were radical utopians who had no check on their power. But this is not merely an atheist problem. One can see strains of this radical utopianism among various Muslim movements throughout the world today, such as the Salafists, whose vision of an ideal society is to live as the prophet Muhammed and his early followers did in 7th century Arabia or the Muslim purists who have recently seized control of large swathes of Mali in western Africa. It all boils down to the belief that you possess the one true way of living and that everyone else is mistaken and you're going to force them to live the way you want them to regardless of how they feel about it. One of the hallmarks of a free, pluralistic society is that you have to accept that some members of that society will have beliefs and behaviors that offend you or you find to be mistaken but who otherwise do not infringe on your personal life. It's the idea that we can all find a way to coexist as long as we respect one another's boundaries.