I don't want to generalise all atheists here since atheism itself isn't the reason I'd have an issue with somebody. If we're talking pet peeves though, there are a couple of things that make me wince.
Sometimes a person will find a particular criticism of Abrahamic Monotheism and think they've found an all-purpose foil to theism and/or religion in general. I suspect this is cultural as if you've grown up in the Bible Belt or somewhere similar, it's very likely you haven't had much experience beyond the dominant religion of that area. That's understandable but it becomes an issue if that view is maintained in the face of contrary information.
The comforting fictions thing that
@Augustus mentioned is also irritating. It's doubly irritating when that same person possesses a starry-eyed wonder at just how gosh darned great humans are.
Finally it's the jokes. George Carlin's invisible man in the sky routine was funny at the time but that joke has since been pounded into the dirt by repetition. It's the Knights Who Say Ni effect. Also, when somebody compares deities to fairies in an attempt to be derisive, it makes me sincerely wish that more people would do some bloody research. It's not necessarily an unfair comparison to make but when somebody does it with sparkly ballerinas in mind they really are showing their ignorance.
Again, this isn't a criticism of atheists as a whole nor is it a criticism of atheism itself. These are just behaviours from some people that I find irritating.