I take it in the spirit in which it is said which usually is to wish me well. If it is response to something they consider blasphemous then they might get a cutting reply.

Say thank you and move on. Most don't mean any harm by it and if they do, it's their time to waste.

Depends on who is saying it, why they are saying it, the location, the audience, & many other factors.
Often asking questions which require thinking is the best response.

I just Thank them and move on

I just say "Thank you, but you can just give me a hug instead."

It is more about them than me. So if they say they pray for me I just politely say: "Thanks." If it makes them happy, or they feel it helps, let them do whatever. Now, if they ask me to go down on my knees and pray with them, that's a totally different story.

I just say thank you and change the subject

After the initial cringe, I ask them if they would mind mowing my yard instead so I can see God's will be done in real time.....lol

I say it is your time, I really do not care what you do.

Thank you. that would be my answer.

I'll think for you...

Personally, I appreciate it, because I know that that is THEIR best, and they've thought to offer that to me. I say "thank you" and carry on. #PoliteAtheist

I think them, because they’re doing something they truly believe people benefit me.

I usually observe that age old adage .. From my schooldays ' well, it's your own time youre wasting ' .

I say thanks, and move the conversation in another direction.

Usually just say "thank you" because I know they mean well, and I don't want to get into a whole philosophical discussion. (It wouldn't be worth it with most of the ones offering to pray anyway).

please don't waste your time on my behalf

I have friends that genuinely believe and dedicate much of their life to help others. I also have acquaintances that use faith as a weapon. If a genuine friend says this I thank them for caring, otherwise I say pray for whatever you want, I'm going to sacrifice a goat, specifically I'm ordering chiva tacos at my favorite Mexican restaurant.

All positive thoughts are welcome.

I'd say it depends on their intentions. If I just had something tragic happen in my life and someone says that while meaning well, I thank them and let it go.

Normally I just thank them. In my own personal experience it's rarely intended as something negative.

It depends on context. It can be an expression of honest sympathy, but more often than not, the specific words "I'll pray for you" is the passive/aggressive Christian equivalent of "Fuck you". Ie; If I tell someone, "I'm going in for surgery tomorrow" and they say "I'll pray for you", I just say thanks. If they ask me if I believe in God, and I tell them I don't, that's the passive/aggressive Fuck you, to which I'll say something snappy.

Depends on how well I know them, but usually it's a thanks but don't waste that on me.

My response to that most of the time is, thank you. I ignore the statement, "I will pray for you," I would rather just interpreted it, in my mind as I hope things get better for you. However, if they are saying after finding out I'm an atheist I will pray for you, I say, "Do what you will, nobody will stop you, but nobody is listening to you either."

Please, just send money. (Sounds like the tactic the religious use!)