I'd have to say in TWW when you awaken either Medli or Makar as a Sage. I can't remember exactly which one it was but the music that they played with their ancestors just reminded me of the old Hyrule under the sea and it just made me feel like I was in that room. It nearly made me cry because some memories of great things make your eyes go watery. The music was just so beautiful and reminiscent of the Hyrule beneath the waves that it was one of those great moments of gaming that has been overlooked.