Flip-Flop of God: Shigeru Miyamoto once said this game could be the sequel to any Legend of Zelda game where Ganon is defeated. Many people saw it as the sequel to Link to the Past, which was the Zelda game released before this one. Hyrule Historia decided to place it after the Oracle games.
Keep Circulating the Tapes: The original monochrome version (which had several Good Bad Bugs fixed in the DX version) was neglected for release for the Nintendo 3DS in favor of the (slightly) newer, color, Link's Awakening DX.
What Could Have Been: Hyrule Historia includes some storyboards that show a few unused elements from the planning stages. For instance, originally at the Southern Face Shrine, the player would have to ram into a pillar with the Pegasus Boots to get the key- the pillar would break to reveal the relief that the player must read. Also, apparently there were plans for a two-player mode, including a boss that one player would have to throw the other onto to defeat. It looks like they were having trouble with what to do to beat the boss with only one player, so the boss was scrapped along with the two-player mode. (The latter concept eventually became a core mechanic in The Legend of Zelda: Tri Force Heroes.)