Came across the list via Hallq. Hope it's not too repetitive.
Why do you not believe in God?: Because with the various hypotheses out there, I'd expect to see evidence, and there isn't any. Other hypotheses don't predict evidence and are thus equivalent to Carl Sagan's invisible dragon.
Where do your morals come from?: Essentially the nearly inevitable consequence that evolution would move towards developing an organism that takes advantage of altruism, a roundabout but reliable method of helping oneself that works for an entire community of organisms.
What is the meaning of life?: That's a meaningless question.
Is atheism a religion?: No. But then, someone will change the definition of religion to temporarily include atheism and change it back when no one's looking.
If you don’t pray, what do you do during troubling times?: Whatever I can to make them less troubling for everyone.
Should atheists be trying to convince others to stop believing in God?: I certainly think so. Truth is important. In addition to that principle, many, many deities people believe in are dangerous, unquestionable authorities and/or amendable to whatever people want to do. If someone thinks it's okay to perform all sorts of hideous crimes, it's easy for them to imagine their deity wants them to.
Weren’t some of the worst atrocities in the 20th century committed by atheists?: Yes. The Soviet Union and China were among them. The problem is that their atheism can't be responsible for it anymore than, say, a lack of belief in astrology or alchemy could be responsible. The problem is that putting absolute authority in a person tends to encourage him to destroy any dissent. It's authoritarianism that's the problem, and religion is one additional source of authoritarianism. I'm very much against authoritarianism.
How could billions of people be wrong when it comes to belief in God?: Because we all share the same faulty wiring that disposes us towards wishful thinking over critical thinking. People used to think that the world was flat, or that the stuff in the sky was made of something different than Earth. American Idol is not a model of epistemology.
Why does the universe exist?: Does there have to be a reason beyond, say, some mindless quantum/string/brane event?
How did life originate?: Probably one of the abiogenesis models still under debate followed by evolution. We're working on it, rather than assuming anything a priori and stopping there.
Is all religion harmful?: I'd say so, but some are less harmful than others, only having some minor damage to critical thinking skills. Others are capable of generating terrorism.
What’s so bad about religious moderates?: Contrary to what most people think, there just don't seem to be that many religious moderates out there: There are a lot of "squishy" pseudomoderates, who like the pseudomoderates Martin Luther King Jr. railed against, only wish to avoid conflict. These are the appeasers who think that having atheists quiet down will quiet down the fundies. The problem is that whenever atheism isn't on the forefront, fundies will continue to shout and lie about us. Thankfully, being an atheist isn't as visually obvious as being non-white so it's been very hard for fundies to engage in such gross discrimination so easily.
Is there anything redeeming about religion?: Nothing that can't be fulfilled through other means. All the literature, music, and so forth can be inspired through other means.
What if you’re wrong about God (and He does exist)?:
A) Omnibenevolent god: No problem, except he'd probably have a lot of explaining to do.
B) Fundie god: I'd be morally obligated to oppose him. Besides, who's want to spend eternity with a bunch of amoral fundies? I'll take the flames over that.
C) Some old forgotten deities: Well, what if you're wrong about them?
Shouldn’t all religious beliefs be respected?: No. They should only be tolerated.
Are atheists smarter than theists?: Not inherently. The definition of "smart" probably needs a lot of debate before we can start.
How do you deal with the historical Jesus if you don’t believe in his divinity?:
A) He may have been a magician who got some tricks exaggerated or even made up. It happened to Randi at least once.
B) He may have been a preacher/teacher/whatever who had miracles assigned to him afterwards.
Would the world be better off without any religion?: Yes. How much better is still open for debate, but I doubt it'd be a utopia. Just better.
What happens when we die?: The worms crawl in, the worms crawl out... but we can at least hope for more as long as we don't mistake hope for evidence.