The most annoying responses are usually in ignorance.
They think because we atheists do not believe in the God they happen to worship, that we could not possibly understand the Bible, that we could not have read it, understood it, and it's the reason we're an atheist?
That when we do bring up a problem or issue pertaining to the Bible, they don't think we understand the context (often better than they do...) it was written in, and try to explain away the atrocities (I've recently learnt that this is what is termed "Christian Apologetics"...If God is good, all knowing, all powerful, and just - then he shouldn't need anyone to apologise for him...). Or hypocritically don't understand that whilst one "bad look" for the Bible (take Slavery for example) can have context that makes it look better, but they then say that the context of other verses (whose content they agree with) is the same now as it was then.
An example is when you bring up Slavery - the usual response is either "It does not condone it" (Er...clearly it does), or "It was in a different context to what we know as slavery now" - err...owning another human being isn't right whatever the context. As though the context makes it okay.
Yet, when it is brought up that the Levitical verses that they continue to use against homosexuality make complete sense in the social, historical and cultural context within which they were written (forging an existence in the desert, need to increase population...how?? Outlaw unreproductive sex), and why do all the other laws no longer apply after the arrival of Jesus but that one? That they say "ohhh, it was "carried over" - why only that one? And why did Jesus have NOTHING to say about it at all in the NT?? Or the Corinthians and Romans verses on the same issue - they ignore the blatant mistranslation (there is NO ancient Greek/Hebrew or Aramahic (sp?) word for homosexuality...but yet many a translation now has the word), all the context that goes with it (and there is a lot), yet want us as atheists to consider the context of the verses they provide?
Not understanding that as Atheists - whether your God exists or not, we don't believe in them, so stop trying to convince us.
And the biggest one?? The misconception that Atheists are inherently immoral, evil and basically only held to account by the laws of the land. Actually, most of us (granted not all) do good for goodness's sake, because we can, and we want to - not because God tells us to.