On my first play through of OOT, one of my favourite moments was Link waking up as an adult, it was just so unexpected! However after loads of playthroughs since, it's become one of my least favourite just because of how much text there is that you can't skip through.
I would say as of now, my two favourite moments are when bongobongo escapes from the bottom of the well ( the cut scene after you complete the water temple ) and being at the Temple of Time when Sheik reveals she is Zelda and Ganondorf captures her.