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".
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!