The first one doesn't make much sense. I'm assuming the second one, however, is suggesting that "she" is odd, strange, or unusual in a way that she does not fit in the same "class" as everyone else. It could refer to social class, perhaps, if she is rich or famous and is therefore in "a class by herself" instead of with others.

These phrases (said either the first or second way) refers to somebody who is outstanding in some way. It could be either good or bad. So if I were talking about beautiful people I might say, "Sally, Jane and Mary are all pretty, but Amy is in a class of of her own".