When Navi goes to a random point and turns green, take out your ocarina and play Zelda's Lullaby or Song of Storms. A golden fairy will then appear fully healing your health and restoring your magic
Impossible you say? Think again! Go to where Lord Jabu-Jabu was as an adult and go to the left hand (master quest=right hand) side of the piece of ice where he was and run along the edge. After a few attempts you will be able to get inside Lord Jabu-Jabu as an adult and you can even active door switches and walk through the whole dungeon. Unfortunately, since the temple was cleared before, you cannot re-defeat the boss or mini-boss.
This is the same glitch as in the N64 version, you need to play the song of storms, then immediately equip the lens of truth. The lens of truth won't use any magic if this is done fast enough.
When you go to visit Zelda at the beginning of the game, look in the window to your right when you walk in. In the original version, there used to be some paintings of Mario, Luigi, etc. However, in the 3DS version, there's something different. There's a mural of a Mario level, complete with blocks and pipes.
When you arrive in Lon Lon Ranch as adult (haven't tested with kid) go into Malon and Talon's House (Cucco House) go upstairs into the bedroom go to the dressers, and smash the two pots. Then go and stand where they were, look towards the dresser closer to the door, and go into first person view. Then, look down and you see a picture of Skyward Sword link slashing with some cool Hylian text in the background.
When breaking out of your prison cell after getting captured, jump to the ledge on your left, take out the guards and smash the wooden boxes. Behind the box is a poster of Link from Skyward Sword.
Skyward Sword posters can be found in numerous other places in the game as well.
When you grow up, and before talking for the second time to Sheik on the Time Temple to learn the Prelude of light, she will tell you that in your home you can rest to revive past battles. That means you have unlocked Boss challenge to fight each boss in the game (after you had beat them in the story) in your house. To unlock the last challenge (all bosses one after another) you have to beat them all in the challenge mode.
Beat the game in Normal mode. Then, after the press start screen, you will be sent to another screen to select between Normal or Master Quest Mode