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Link's trekked across the land, survived forests and deserts and even walked on water, all to deliver six crystals bequeathed to him by an ancient king. He's beaten the Thunderbird and then faced off with his own shadow. The moment when the Triforce of Courage descends into his hands, marking him forever and always as the Chosen One, is definitely a CMoA.
The fight with Thunderbird itself, in which you blast Thunderbird with the Thunder spell.
The second the magic barrier dissipates and Link enters the Great Temple accompanied by the atmospheric music makes for an awesome scene.