I personally don't see the point in being rude. I know they mean well, so I smile and say "Thank you". Some people need faith as a crutch, and I don't feel the need to yank it from them. There is enough meanness in life and most of us have a weak spot somewhere.
Admittedly, I have some obnoxiously evangelical cousins, and I have had differences with them when they reach for their bible, but if someone is atempting to be nice to me, why would I mistreat them?

I guess it just depends on the context in which it is being said. If it is sincere, I usually just say thank you and go on with my life. I have only had one person tell me that they would pray for me and mean it in a pretentious manner. I had gone to the local planned parenthood clinic, because my regular doctor was out of town, and I needed to be seen. As I was leaving there was a group of people protesting the clinic outside chanting and trying to give out religious pamphlets. One woman tried to hand me a pamphlet and I told her no thank you. She gave me a pious look and told me that she would pray for me. I told her where she could stuff her pamphlets.

It's not worth making waves usually.
I just say thank you when they say they will pray for me.

Thank you everyone for your responses! I'm new to the site, that was my first post, and you guys made my intro here pretty damn cool..

They can pray for me all they want. Whatever gets them through the night. Where I draw the line is if they ask me to pray WITH them. That is when I will tactfully tell them that my beliefs differ greatly from theirs and thanks but no thanks. If they attempt to pressure me, then it’s no holes barred. There is a difference between offering consideration to another human being (which is what I consider prayer anyway) and being a pompous, condescending, patronizing, sanctimonious jerk trying to cram your beliefs down someone else’s throat.

I either say thank you and move on or just ignore them.

No thank you.

Anyone who says that to me likely knows I'm an outspoken atheist, so they don't mean it as an affront to me, but genuinely think praying would help. I generally say something like "This atheist thanks you for your kind thoughts and good wishes."

If it makes them feel better, fine, but it does nothing for me. Telling a Christian your real opinion is usually a waste of time, and then they are apt to start proselytizing, and I don't suffer that.

It is rather unsatisfying to argue with the chronically religious insane.

"Thank you! When I get home I will sacrifice a goat and pull through its entrails to see what I can find out about your future." That seems to set things straight.

I swear the next some religitard says "I'll pray for" or "God Bless Your" speaking of terminally ill brother, I'll crush their fucking nose..

It really depends on who it is, the context in which it's said, and what my mood is when I hear it.

Life is way too short to take such things personally. When the sentiment expressed is somewhere between perfunctory and well-meaning, I see no reason to deconstruct and debunk it. I'll take well-intended kindness in whatever form it comes. As for "I'll pray for you" as passive-aggressive condescension, I'll overlook it in most cases, it's not a hill I choose to die on. If, hypothetically, someone made that part of a proselytization play, I might, if in the mood, mention that I've had terrible luck with prayer and gave up on it long ago, but suggest that they can ask god to cure my diabetes and I'll be sure to inform them when it happens.

I might not believe but I would never be rub to someone who does

I'm not rude but tell them to please not bother

It's nothing more than a platitude; a social lubricant to escape a difficult situation. The religious spout this nonsense to appear caring and pious. Yeah, I'm senical about this, but it is excruciatingly annoying.

Basically keep my thoughts to myself, and try to hide the visceral flinching it makes me feel inside. I don't see a need to make a big deal about it.

I usually don't get into debates with people about it. I may tell them I'm an atheist, but I usually don't go far past that.

I take it in the spirit in which it's given. It won't change anything but it shows that the person cares.

I just say thank you and move along unless the offer was sarcastic or downright rude in intent. Prayer isn't meant to be a weapon of shame.

My usual response is "I don't believe in that, but I guess it can't hurt".

Pray for me, and I'll critically think for you.

I slowly back away. They are probably quite ill.

When people sneeze I dont say bless you and I tell them that I dont say that because I`m not the pope.