Could you please tell me the difference among them.
Thanks in advance
The standard in American English is "It's fine with me."
Personally, I have to say that "It's fine by me" strikes me as an old-fashioned expression and/or very informal.
I don't know anybody who uses "It's fine to me". However, the following are common:

It looks fine to me.
It sounds fine to me.
It seems fine to me.

These three would not take "with" or "by".
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Could you explain the reason why you can use "to" for those three sentences but not "with"?
Yes, I can. Emotion: smile
with can imply if it is with.
It looks fine with me thus means It looks fine if it is with me. The real-world situations in which you might mean this are extremely limited!