…and you’re not a believer, here are some appropriate responses from Peter Mosley at Patheos.
This comes from an earlier conversation I had with Dan Blinn, lawyer, humanist, and a hell of a good guy. My reaction to someone who says “I’ll pray for you” is to respond “And I shall pray for you,” and then I make a big show of getting their name so that I can pray for them personally. This is a completely non-Christian up-yours response that I should probably work on but don’t.
Dan’s suggestions — via this article — are better.
Dating Jesus 
I always just ask for a first name of the person who I will pray for if I do not know their name
Before I read the article, I’ll just say: I’m an agnostic who believes in and tries to practice kindness. When someone (who is not employing snark) says “I’ll pray for you” I’m mostly complimented because they’re offering something that’s serious to them and generous and thoughtful to me.
I accompanied a friend to the clinic pharmacy the other day to get our meds and review new clinic procedures. As we sat and went through the handouts, a woman about my age sat down next to me. We began to chat. Before long we were exchanging healthcare horror stories. When I bested her with the story of my last hospital stay she patted my knee and said, “That’s a trial. I’ll be sure and say a prayer for you.”
“Don’t bother,” says my friend. “He’s an atheist.”
Her palm shot to her mouth as embarrassment flushed her face.
“I didn’t mean to…”
“That’s all-right,” I said Thanks for the concern.”
“I didn’t think you people liked that sort of thing.” She sounded relieved.
“I’ll accept a kindness from just about anybody.”
“He’s a Socialist, too,” my friend chimes in.
Well then,” she grins, “I guess I’ve got my work cut out for me.”
We all laughed.
My friend leans in closer and half-whispers…like it’s a secret or something, “Folks been prayin’ on This One for years. Doesn’t do any good.”
“Well, she said, “You never know.”
“That’s right,” I agreed. “You never know.”
LOVE this story! :) Thanks for sharing.
Leftover’s story made me think of posting this to share here. I liked this part:
“Well, how old were you when you figured out, all by yourself, that ‘The Little Engine that Could’ was both not true, and absolutely true?”
Sometimes, the meaning is more important than the words.
http://www.ucc.org/daily_devotional_sometimes_play_is_work