>>You're thinking of her ?
>>
>>Or your thinking of her?
>>
>>I would assume only these two forms are correct?
>
>It's the context that matters. You're thinking of her is "you are thinking of her" and doesn't fit the context of the statement I posted. "Your" is correct. See my reply to Gregory. If we change the statement to read "She'll appreciate the fact that you are thinking of her..." then substituting "you're" would be correct.

Yes, that's exactly that I was thinking.