The Wind Waker is a sequel to Ocarina of Time. In Wind Waker Ganondorf tells you that he met you before, or at least One like you. He's referring to the Hero of Time who defeated him long ago, and the new hero, the Hero of Winds (you) are the next in line.
Without confusing you, the Zelda series is like this: The first game story, Skyward Sword, tells how Link's spirit will be reincarnated and the Master Sword will obey him again in another life. That other life is Ocarina of Time, and OoT has 3 outcomes - Link defeats Ganon, the sages seal him in the Sacred Realm, and Zelda sends Link back to the past to relive his stolen childhood. As a child again Link prevents Ganondorf from betraying the King and Ganondorf is imprisoned and the future is altered (leading to Majora's Mask and the Gamecube titles)
BUT in the future where Link defeated Ganon and the sages sealed him away and Zelda sent him back to the past, Link is GONE and Ganon eventually escapes his seal and returns to wreak his vengeance on Hyrule. With no hero to stop Ganon (because only the Master Sword can do that and Link is the Only one who can use it) the people pray to the gods for help, and the gods respond by flooding Hyrule and sealing Ganon away with it. That's all in the prologue of the game but now you have a better understanding. Ganon escaped that seal again and set about the events of the Wind Waker (followed by the DS games)
The third outcome involves Link losing to Ganon at the climax of Ocarina of Time, which leads to A Link to the Past, the Game Boy games, and the NES games (in that order)