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A side note; I don't care for the term "non-believer" (speaking for myself that is) because the definition of a non believer is: 
"...a person who lacks belief or faith, as in God, a religion, an idea, or an undertaking. ..." and the listed synonyms for 'non-believer' is
 "...doubter, skeptic, questioner, cynic. ...", none of which applies to me. Some people tend to think if we aren't judeo-christian we must be non believers, when in fact I do have my own personal beliefs and religious views.  It's hard to describe,  but according to my beliefs, I don't think others who believe in God are wrong (which would be to NOT BELIEVE them), I think we actually could all be right in our own individual beliefs. Basically, I am a believer, just in different things, if that makes sense. I am Buddhist, so I am very much a believer... in Buddhism. Just don't worship the God that others do. Not that anyone asked me, ha ha, I just thought I would share that perspective.
But to answer your question PK, I typically respond that I will be meditating for them (which for me, is putting my thoughts and positive energy out into the universe as opposed to asking God for anything) or I simply say I will be sending good thoughts their way, or that I am thinking of them. When it comes down to it, I think (hope) that people are comforted either way, whether we are praying or just sending out good energy. Both, I believe, are very powerful.
I stand corrected 
I was just referring to me, Deb. I'm sure lots of people consider themselves non believers. I was just blabbing.