@Dark: I think the jury is split on whether or not Gender-changing magic is possible. I believe Trixie's exact words were "But that's impossible", or something to that effect - but at the same time, she could easily be exclaiming disbelief that Twilight could do it, not that it could be done at all. She certainly seemed aware that the Alicorn Amulet didn't make her
all powerful, I think, just extremely powerful.
Some time ago in the LGBT thread in Yack Fest, I and another fellow sort of co-opted an idea for a fanfic based around gender switching magic. The idea was that Twilight was trying to adapt the Butterfly Wings spell into a spell that would temporarily change a pony's race. A rune was mixed up in writing it, however(This is at a time when "Twilight botches a spell" was not quite so cliche, and at that there was a difference in that the spell was cast perfectly, just worked differently from intended. Like a line of code that causes a program to perform a different function than intended. I once wrote something intended to teleport a red square on contact, and wound up duplicating it), and the 'unfortunate' target of the spell wound up being temporarily turned into a mare... something 'he' was not in fact displeased with. She then spent a while gallivanting about in her new mare body, and met a handsome young stallion... she then found herself repeatedly going back to Twilight to refresh the spell. After a while her body would start to adapt to the spell, and it would be less effective. Eventually her new boyfriend, who was an actual doctor, would find out, and start working with Twilight to find a way to make the spell permanent.
So basically, a story about Equestria's first Male-to-Female transexual operation.