Enised's The Mathias Prophecies, in which Harry turns out to have been a girl all along - I mean, not transformed by magic at any point, but just born a girl. Some readers complained that the idea was incredible, but as I know instances of people who managed the same deception all their lives long - and without magic - I don't particularly see that. The trouble is that Esined made a total botch of the leading characters, turning Snape into a good guy, Dumbledore into a soft oversentimental fool, and giving Harry a new extra power with every episode. Her cliffies and climaxes are good, powerful and unexpected, but you have to wade through a lot of stuff that simply does not work in order to get there.
I just might have a go at it myself, just to see it done right, but I would have to find a reason for the concealment and a suitable development once it is discovered, and I must admit that - as in the matter of her climaxes - Esined has come up with a good reason for the one and a good development for the other.