If they are being kind I thank them. If they are being judgemental I tell them to fuck off lol.

I just say thank you. But what I want to say is it would be more useful to order pizza.

I say "thank you" if anything. Discussing or insulting someone ignorant for doing what they think would help you is, I think, cruel. It's like having the flu and abusing someone for telling you to put cloves under your pillow. Ridiculous but at least the person is showing some caring.

I tell them I find it offensive if they know I am an atheist.
They are disregarding, belittling my lack of belief and therefore disrespecting me.

You pray for me, I'll think for you.

I typically ignore it. I understand that they have been inculcated and conditioned to say the catchphrases of religion without thought.

If I ever have the opportunity to discuss it (rare) I will ask if their deity has a plan and already knows the future? If they say "yes", I respond with, "Then why pray? You think your deity is going to change his mind/plan with your prayer?"

I say save your prayer and donate to a charity

I forgive you

Thanks, but it won't help

I would thank them for their uselessness and walk away. Prayer is like peeing into the wind ... all it does is make your body wet

I would just say ok. Everyone who knows me knows I'm atheist so there's no need to start up a debate about it. If someone feels like praying for me woopdedoo. Whatever works for you. As long as they don't ask me to pray with them it really doesn't have anything to do with me. I don't care what other people do. I think most of the time they don't mean it anyway it's just something people say when they don't really have a response to whatever you're talking about

"And nothing fails like prayer"

I just say thanks but No thanks..

if it's a general I hope you feel better, I hope things workout for you, I wish you luck sort of thing, I say thanks.
If it's you need to think or act differently or behave in a way they prescribe, then I tell them I hope they mature out of this phase. Or just generally, FU if we have already had the conversation.

Thank you all - this made me smile in a rueful sort of way. When my husband hears this he thinks 'that's nice and caring' ( but he isn't an atheist/agnostic) . I take a negative view, but I think I've only heard it directed at my children and not myself and it made me cross when I went to the form teacher with concerns for daughter's happiness and advice and I got 'I'll pray for her!' . I think it means ' Oh Dear, well I don't know what to do/suggest and I don't intend to do anything, but I'll feel good about myself for being nice'. Maybe they mean by 'they will pray for X ' that they will reflect on it. That's good, but if it were, then I would expect them to suggest some kind of review or course of action. I suspect it really just means 'I'll do something nice (pray) and then forget about it as I feel impotent or uninterested'. SO I'd like to say something mean and witty, but I think I just shrug and say 'if you like'. They don't know any better, so not worth pursuing, at least you know not to waste your time seeking help there.

I'd say, "Your god planned this, don't fight"

"Thanks." Then I change the subject.

Generally they get a flat smile, but if they seem to need something more to get them to move on, I give them some kind of pleasantry. If they say it to be rude, condescending, or something to that effect, they get a genuinely amused look because the irony gets to me every time.

Just say thank you. They mean no harm, in most cases they think they are helping. Makes them feel better.

I have been told by a friend who is a Christian that she prays for me. My response has always been that she is welcomed to however I find it condescending and disrespectful to my beliefs, which she is very much aware of, and if she wants to persist in praying for me, not to tell me.

Woah, soooo much negativity around that question! I really believe that most people have good intentions when they say it and honestly because sometimes it is hard to find words to comfort someone. I have had people say that to me in a condescending way and I try to remind myself to say back that I will pray for them for demonstrating the sin of pride...

I have said on more than one occasion, I appreciate the sentiment but I respectfully ask that they not do that or speak that way to me because it has reflected as a curse in my life many times.

It kind of depends. The last time somebody said that to me it was their way of saying that they thought I was living my life wrong. In that case, I just ignore it rather than tell them to f off like I want to. If they are saying that they are hoping to reverse something that has gone wrong, I say "thank you" because my mother taught me to be polite.

much like when someone says bless you when I sneeze, I say thanks. They are probably just making what they consider a polite noise

How it is said means a lot.

I have heard it said to me with solemn sincerity and good intentions, no matter how misdirected I might find it. There are others that practically speak the phrase as a weapon, dripping with condescension. There is an entire spectrum possible between.

When kindly offered, I might respond, "I appreciate the sentiment, but I am not religious at all. I would prefer that you did not, but do as you like."

Various levels of snark may be unleashed depending how irritating they are or how long since my last meal. For the most egregious offenders a righteous and profanity-laden monolog might be unleashed spelling out how unpleasant others might find their behavior.