It's a fan development started as a sort of project by regular posters at the Animesuki forums, but has since then taken a life of its own. It's scary, don't you think?
Fencedude said: Except for the part where it didn't start on suki.
To be more precise, it's stated in the thread,
AnimeSuki said: Much of this fan fantasy has been derived from the various image posts that been found portraying the characters of the Haruhi universe as the opposite sex.
The project came AFTER the idea. The original idea is not AnimeSuki's. In fact, I don't even think anyone thinks of animesuki when Kyonko and crew show up.
Also, post #127796 is one of the oldest genderswap Kyon images that I know of [quite a different design from the standardized Kyonko design we see nowadays], and it's probably over a year old by now. The original idea must have started way before that.
If I'd have to guess, I'd say the idea probably started on a Japanese imageboard.
