It can't really be done. You get the credits, it shows Link and Zelda, states that it's the end, and then you either get the title screen again or have to reset the console to resume gameplay. But as far as saving it after Ganon's been beaten? Not happening. Sorry. Otherwise, you'd be playing in a monster free, boss free game. Which... they didn't really program it to do.
If you've only beaten the story on Ocarina of Time I would recommend finishing the side quests as well (Pieces of Heart, all upgrades [Magic, Wallet, Weapons, ect], all 100 Gold Skullutas, ect.), if you've done that, you could purchase or play through the Master Quest version of Ocarina of Time and 100% it too. Timelinesplitter 01:46, June 4, 2012 (UTC)