I've been reading the Minefold blog and therein found the following:
During a fireside interview at the Game Developers Conference in San Francisco last weeek, Minecraft creator Notch dropped an extremely big surprise on the Minecraft community.
There is still one hidden recipe that has yet to be found.
It’s hard to believe with all the modding and customization that has been a core feature of the hit indie title hasn’t revealed this mysterious unknown crafting recipe.
Best Answer
The secret wasn't a recipe:
Here is Notch talking about it on reddit:
Source: Reddit and Planet Minecraft