I would definetly say the following:
1) Link pulling out the Master sword in OOT, only for it to be revealed that Ganondorf actually snuck in behind him and stole the Triforce (of power), with Link then going into a seven year slumber and ultimately growing up as is shown in the next scene when he is in the chamber of sages. I think that was very momentous in symbolizing Link reach a milestone of growing up and starting coming a long way in his journey, as well as really setting the scene for the catastrophe that is befalling Hyrule.
2) The ending scene of OOT where Link and Zelda are in the sky after having defeated Ganondorf and are bidding goodbye. It is very emotional and bittersweet, as Hyrule has finally been saved, yet Link and Zelda have to bid goodbye to each other, with some implied romance between the two, and Link being ultimately sent back in time, not being remembered for his heroic deeds and leading to further trouble for him in the following events that take place in Majora's Mask.
3) The scene in Twilight Princess after Link has just defeated King Bulbin for the first time, and he sways majestically on Epona, symbolizing that the Hero of Twilight/Hero chosen by the goddesses has been born, with pretty epic music playing to go with it.
4) The ending scene of Twilight Princess with Ganondorf, where Link impales Ganondorf with the Master Sword, Ganondorf screams, stands up with the sword in his chest, looks at his Triforce of Power hoping it to save him, only for it to abandon him, with Zant then, from an apparent afterlife, breaking his neck, killing him telepathically, with Link and Zelda standing next to him staring in shock. That was indeed very epic and intense; the best, most momentous end to a final boss, with him actually having been explicitly killed, in such an intense kind of way as well, through both impalement then telepathic neck breaking which was pretty messed up, and pretty cool having his own minion contribute to his death.
5) In OOT when child Link arrives at Hyrule Castle, about to deliver the spirtual stones to Princess Zelda only to see Zelda and Impa ride away on their horse while Ganondorf is in pursuit of them, as Zelda throws the Ocarina into the moat for Link and then Ganondorf appears, ambushing Link and announcing his evil intentions to rule the world, who shows his bravery as he gets his sword out, only to be pushed back Ganondorf's sorcery. This was amazing as it showed the start of what was going to be a real catastrophe, but without us knowing just yet how this would happen, we still felt that fear and intensity arising, and what the rest of our journey would involve.
6) Entering the room with Ganondorf in playing his theme on his organ in Ganon's castle in OOT, ready for the final boss fight. It really sets the scene, having finally reached the climax of your courageous journey facing evil, as now you are facing the ultimate king of evil, with Ganondorf perfectly symbolizing the fear, darkness and evil here, as you have finally reached the peak of the tension after having gone through his castle with the very tense music playing to discover he was playing it all along of course!
As you can probs tell, these are my faves games of all time, particularly OOT! Twilight Princess I think is rightly known for its cinematic scnes, which I love, but OOT is my ultimate favourite, so overall I think that would still win in my books!
