"Thanks. I appreciate it."
Everyone who cares about you will have their own way of expressing their best wishes for you. I don't fret about the words they use to say they care and like me; I'm grateful for the message and affection.

I just ignore...

I usually say "couldn't hurt".

I just ignore it. They think they are beign well intentioned and have no ill will. Let them have their happy fantasies.

Be appreciative with a polite smile . . . unless it goes like this: "I'll pray for you coz you're such a badass you don't believe in God!"

I worked in retail and would get that too. I typically didn't need to respond to it but maybe a slight smile and a head nod. If they just learned that I'm an atheist in a non professional setting and said "I will pray for you" I like to respond "and I will think for you" and just leave it at that.

"thanks"

just say thanks and move on. I take it as them saying "I wish you well".

I thank them and go back to what I'm doing. You need to pick your battles.

SamL has the right approach, in most work or social situations there is no need to be confrontational, and it doesn't get any converts to atheism to be nasty.

A simple thank you suffices. No comment beyond that is necessary unless you're looking to spar. I say thank you and then get on with it.

I just thank them for their good wishes, no sense in being angry at some one that wishes you well.

thanks

The cheekiest response is "Thanks, I'll think for you!" But the probably appropriate response is just "Thank you, I appreciate it." Most of the time when I hear this, it's not because they're being malicious or anything, just offering sincere concern and well-wishes, so I treat it as such even if I don't share their beliefs.

I thank them, assuming I believe they're offering it in a generous light. There is no point, in my opinion, to allow yourself to get offended. It isn't their intent to do us harm, but that's just my opinion of course.

It's either one extreme or the other lol. "Thank you, whatever makes you feel better (and for caring about me in some way)," or facepalm "it's not like it f***ing matters, you idiot!"