She really is beautiful.
In this case, really modifies 'is.' This also makes 'is' the focal point of the sentence and will likely receive emphasis. "She really IS beautiful!" This might be said by someone who is stunned or surprised by how beautiful she is.
She is really beautiful.
In this case, really modifies beautiful. This is to state that she is not just beautiful, but really beautiful. She is more beautiful than a person who would simply be considered 'beautiful.'
She is beautiful really.
This is a somewhat uncommon way to express it. This would generally be used in a situation where what is observed isn't necessarily reality. For instance, if you see a girl who is a mess, hair all crazy and wearing strange or old style clothes. Your friend might say "Wow, look at that girl. She looks so crazy." but if you actually know that she is beautiful, and that's not her normal or her best look, you could say "She's beautiful really." (with or without an explanation as to why that is)
A comparable statement might be "Actually, she's beautiful."