It's not hard to find a fantasy or sci-fi piece where the hero is made out to be the villain. It tends to have some downsides though, such as the hero getting the benefit of an enemy he has to completely destroy and his not having to stick around and face the same people every day. The hero can and often does travel.
Are there any that are done in a more "real" setting? Particularly a school, as I mentioned, since the guy is then faced with the same people every day, and inevitably is also stuck close to the real villain as well. And youths jump to conclusions quickly and hold to them, meaning that a smart enemy doesn't have to do much to convince others that something happened the way he says, and it can be very difficult at times to convince people otherwise without clear evidence.
One thing I'm particularly interested in is a story where a student who's average or even popular is framed or falsely accused of some horrible act, such as rape. While it would be easy enough for him to prove that there's not enough evidence to convict and thus that he's legally "innocent", it would take a good deal of evidence or character to convince most of his fellow students. A great new anime this season has something similar happen to a girl.
In a way, this could almost be called social rape, in the way it affects the person and leaves marks that are very difficult to heal.