Urban Legend of Zelda: Several; the many glitches in the game coupled with the tons of Guide Dang It content has resulted in many theories about things hidden in the game that are just very difficult to unlock.
The Magic Gourd, according to Word of God, does nothing. Theories still abound though about what it was intented to do, or even that is does do something and the developers just don't remember. The most common theory is that it boosts the power of offensive alchemy, as Magic Attack is the one stat that doesn't have a matching Charm to boost it; the catch is there is no Magic Attack stat.
There are only two alchemy ingredients in the game you can't buy normally — Dry Ice and Meteorites — that are used in one spell, Call Up. The ingredients are found very rarely throughout the game, but rumors are that there are merchants who carry them, they're just very well hidden and only appear under certain conditions.
The Oracle Bone is described as changing what certain NPCs say to you. Only one confirmed instance of this occurs in the game, and it's just to make an alchemist give you an alchemy formula at the end of the game. Given how arbitrary this seems, cue speculation on other dialogue changes the Bone influences that just haven't been documented yet.