When I was a kid there was a documentary about the early settlers coming to North America and the history of Thanksgiving; at one point a Native American who befriended a colonist asked him to pray for him the colonist responded that he can't pray to the native man's god and the Indian responded not to my god but yours.

My question is what happens if you pray for someone who worships a different god or goddess? For example: what happens if I pray to God that he helps someone who is apart of the Hindu religion?

I wouldn't worry about it. I had a friend once ask me if she could pray for me on occasion even though I didn't believe in it. She was leaving to live somewhere else and I thought it was a sweet gesture on her part and so I said sure! I mean why not?!

She wasn't wishing me ill or trying to hurt me in any way and it also didn't feel like a weird, "I will convert you..." type of vibe and if it made her feel happy then why the heck not?!

I think it doesn't change anything , in the end your god is your god and the other person has its own religion and god.

The most important thing in here is not the difference of religion it is the intention you put to your prayer. The power of will is the one of the most powerful tool.

In the end, the good intention will find its way to the other person

So I have a deeper take on this, and some may or may not like this answer. I think this depends on the deities in question.

There is a general consensus, and an incorrect one, that "God" is always good. But there's constant reminders throughout all scriptures that "God" does terrible things. This is the case in pretty much most monotheistic religions. It is DEFINITELY the case in polytheistic mythologies - there are almost always good and bad sides to every deity.

The point? What does your prayer ask your god to do for the other god's follower? Bless them? Why would they, especially if they don't see eye to eye or have been past enemies with that person's patron? Would this act of favor toward another bring reversal of fortune upon yourself or hurt your own relationship with your deity? I can't answer that, but I think it's a valid question. Some may say, "But God is altruistic and would honor this request in the spirit it was offered." Would they really, though?

The other thing I like to think about is what will the effects of my prayer be. Say I am Christian and I pray for someone, out of the kindness of my heart, to find Jesus - for God to guide that person to believe in my God. Say the person who you are asking this for is pagan and they have no intention of accepting Jesus. At what point does this prayer become a curse? What if it causes immeasurable strife in that person's life by interfering in their pathwork, because you "want the best for them", but YOUR best isn't their path?

I'm not bringing this up to debate religion, at all, and I don't intend for this to become a topic of debate. My point is, if you are going to pray for someone that does not believe the same you do, think very carefully what kind of impact that might have on their lives and your own. For example, perhaps the prayer needs more specificity, or perhaps it simply shouldn't be made at all.