I long ago decided that since I don’t believe in any god, saying “God bless you” or even just “bless you” was inconsistent and potentially gave people the wrong impression about me. So I always say “gesundheit.”
What do you say?
I say, “Soul, get back in that body.”
“Salud”
A combination of the first three, depending. The wife and kids get “Bless You,” most other people get “Gesundheit,” and students get “Get away from me, you disease-ridden plague-monkey!”
I’m an Agnostic Areligionist, so hopefully that’s close enough to Atheist…
I usually say ‘bless you’, but it is more a reflex than any conscious think about it. Like saying 'oops ’ (when you drop something) or &(*^^%^& (when you drop something on your toes).
I say, “You know, when you die, you’re just going to end.”
Kidding, I do the gesundheit.
Oops! Frodo has exposed my USA-centric bias. 
So if you live in, or are from, an area that has a different standard sneeze response from the ones I’ve listed, please mention your location, whether your reply is the usual one there, and if it is not obvious, what religious overtones any of those replies may have.
Something that is a combination of “gesundheit” and authentic frontier gibberish.
“Gesundheit” is assumed but actually not fully articulated.
I say bless you. I just don’t care. And I am a strong atheist, which means I’m pretty positive there is no god, at all, not even a Deist type of hands off god. But the social convention is to say bless you, so I do it, and I don’t even think about it twice.
Agnostic polytheist, but I say “gesundheit” for the same reasons as the OP. If I sneeze and no one says anything, I announce that the demons are getting in, and could someone please help?
‘need a mop?’
You are sooo good looking.
I don’t say anything.
I’m Dutch and like ze Germanz we just say "Gezondheid’. If it’s in an international environment, I say “Bless you” regardless of my atheism.
I’m the athiest atheist and I say “Bless you.” Mostly because it is what is considered to be the polite response dictated by my society. Much like saying “Good morning” or “How are you” when you first meet someone during the day. To me they are all polite expectations that are semantically null.
This. Though I often say, “Jesus Christ, cover your fucking mouth when you do that.”
I either say nothing, or an occasional “gesundheit.” Conversely, if I sneeze and someone says, “bless you” to me, my usual response is, “excuse me,” as opposed to, “thank you.”
“Gesundheit”. Sometimes followed with “Hey, everyone, stay away from [sneezer] – s/he has Ebola!” (There’s a long history of Ebola jokes at my office.)
"snort I guess your God didn’t protect you from the common cold, did it? Eh? Did it?*"*
And then I try to push the Richard Dawkins books I always carry with me on the unsuspecting victim.
“Bless you”. For pretty much the same reasons as Cyros. Pure social reflex. I also say “goddammit!” when I stub my toe or hit my head, from the same reflex.