Ah, that's why the flute sounded so familiar.... it's from SMB3! I knew that that was from another game, but I couldn't think what. I never noticed that it was at the beginning of the OoT theme either. Interesting observation.
Courage is like love, it must have hope for nourishment.
Wow, their the same. Its so amazing that two games with the same composer would use the same song.
And the Flute in LttP sounds nothing like Saria's Song. It sounds slightly like the Song of Storms, if anything.
I love how Nintendo hides those little comparisons in between its games. As for those specific examples, I had never noticed that they were the same tune in the Zelda OoT title screen, though I did hear a similarity.