u could do what i do

its pretty aggressive but effective

i respond by saying "thanks ill fuckin pray for u too!"

I'd be honest and say "I'd rather you not, but if you feel that strongly, then please do so in silence, because having to listen to prayers would make me even more upset." I prefer to handle any crisis with human reason, compassion, self reflection and time. I don't want to perpetuate belief in supernatural deities.

I would say I appreciate it ,thanks.

Depends on who it is but some people I would just tell that your prayers may make you feel better but they won't help me one damn bit.
Others I would just thank.

I politely nod and say ok they mean well no need to be mean

If I'm put off by a well-meaning expression of sympathy merely because it contains elements of a worldview that I don't believe in, my personal crisis probably isn't terribly severe. I just thank people for their kind words.

Won't work but sure can't hurt

I shine it, no point in opening Pandora’s box, I just say nothing at all to encourage it. You can tell when they mean well, it feels different when they’re manipulating you, if I say something it’s when I feel manipulated.

I’d say “thank you, that would be kind”…but it would only be a stranger or someone of very slight acquaintance who would say that to me, because all close friends and family know I don’t believe in god.

Ummmm, "thanks"?

I take it in the spirit it was offered. If it was offered in lieu of offering help, I just ignore it, if it was offered with the expectation that I would seek and receive help from them, I thank them, then if they can actually be of help, I might ask them for it. If it was offered because they didn't know how to respond, but want to say something, I thank them and go on.

Hopefully they won't have an reason to pray for me.