To understand the revised theory about OoT's ending that I'm about to put forth, you should be familiar with my last article on this subject (OoT's Ending, Revisited) and the recent article Hyrule's Geography. Now, read the following theory and feel free to comment on its validity by e-mailing me or posting in either of my forums.
OoT's Ending and Beyond
When Zelda sends Link back in time at the end of the game, he is sent back in time as usual, to the time after Ganondorf has already entered the Sacred Realm. Zelda has told Link to "lay the Master Sword to rest and close the Door of Time," since by doing this "the road between times will be closed." Link knows he must not use the Master Sword again until seven years have passed, or risk traveling to the future again and causing odd time paradoxes. He leaves the Master Sword in the Pedestal of Time and, taking the Spiritual Stones with him, closes the Door of Time.
Link knows that he can still change the future, though. He goes to see Zelda, who has returned to Hyrule Castle because Ganondorf isn't after her anymore. Link warns Zelda of how Ganondorf will attack the castle in seven years, and she prepares Hyrule for that day. She lets Link keep the Ocarina of Time as a keepsake. Link gives the Spiritual Stones back to their owners, and entrusts the Spiritual Stone of the Forest with the Knights of Hyrule. (In ALttP, Sahasrahla says, "These Knights of Hyrule were also guardians of the Pendant of Courage.")
Link, a great peacemaker, departs for adventures unknown on his horse Epona. Months later, while riding through the Lost Woods, Majora's Mask happens. Seven years later, as the Sages try to find Link so he can wield the Master Sword, Ganon's army attacks the castle. Link is prevented from using the Master Sword because doing so would reopen the path between the present and the future. The Knights of Hyrule fight valiantly and lose many of their number, but since the Sages this time are not imprisoned in their temples, they are able to seal Ganon in the Golden Land, ending the battle.
After the Imprisoning War, Link and the Sages, foreseeing the Great Cataclysm brought on by Agahnim, reshape the Spiritual Stones into Pendants of Virtue and hide them in dungeons. When Hyrule Castle is moved from west of Death Mountain to the center of Hyrule, the Temple of Time is also torn down, and the Master Sword is hidden in the nearby northwestern Lost Woods, stuck into a new pedestal. It is protected by magic, and can only be pulled by one possessing the Pendants of Virtue, the legendary Hero of Hyrule. It still guards all entrances into the Dark World. Over the centuries the Lost Woods grow, and the Master Sword is concealed deeper and deeper in the forest.
During this time of peace, Ganon opens an eighth portal to the Dark World on top of Death Mountain. Many use this portal to enter the Dark World, and this way Ganon obtains the whole Triforce. Once Link pulls the Master Sword in ALttP, all warp tiles leading into the Dark World open up, and Link is able to use them once he finds them. When Link defeats Ganon at the end of this game, the Dark World disappears and so do the warp tiles. The Master Sword rests in the northwestern Lost Woods, never to be used again since its purpose has been fulfilled.