Starred Game mode:
Beat the game to unlock Starred Game mode.
Alternate ending sequence:
Beat the game two times to get bonus mail after the ending sequence.
Bird to ninja door:
When you get to the machine that you have to spin, notice the bird flying through trees and landing on branches. Once you complete the game and have a Starred file, return to this machine to see that it has changed from a bird to a ninja.
Legend Of Zelda easter egg:
Before taking t he white book off of the bookshelf in the silver bird room, select some of the other books to find one titled “The Legend of Zelda: A Chronology.”