The Official Nintendo Magazine has a new article which quotes Miyamoto as stating which Ocarina of Time Song is his favorite. The following quote was in the inlay of the Ocarina of Time 3D Soundtrack should make it obvious which was his favorite.
“Music is essential to the majestic world view of The Legend Of Zelda. Music has also come to play an important role by being associated with highly individual characters in the game. This game, which centres on Link playing the ocarina, allows the creation of many different songs by repeating these notes. Epona’s song, sung by Malon, stands out as particularly memorable.” – Shigeru Miyamoto
For those of you who did not read his quote and just want to know which was his favorite song…it is Epona’s Song sang by Malon.
Miyamoto further expanded on his reasoning with, “This game, which centres on Link playing the ocarina, allows the creation of many different songs by repeating these notes. Epona’s song, sung by Malon, stands out as particularly memorable.”
