The famed intro, which is the single most respectful and perfect homage to the series as a whole. Ganondorf's reign of terror is at its peak, and the mournful violin music fades with the hopes of Hyrule...then it kicks in with the Zelda theme we all know and love, as a young boy vanquishes the evil.
The beginning of the game, when Aryll is kidnapped and Link actually tries to jump after the bird who did it from over a cliffside. And, right afterwards, Tetra grabbing his hand at the last second before falling down, telling him "She's gone, you idiot!! There's nothing you can do!"
The heartbreak that accompanies this scene simply makes the later CMoA where you destroy that damned bird, complete with a kickass explosive death scene, all the greater.
Link's first face-to-face encounter with Ganondorf: Ganondorf has Tetra forcibly caught, and is about to take her Triforce from her — when all of a sudden Quill and Komali swoop in, fly her and Link out of harm's way, and then Ganon sees Valoo out his window... before Valoo torches the place down in one blast.
Valoo may have stole the show but special props need to be given to Komali in that scene, having gone from sulking in his room earlier in the game to grabbing Tetra out of Ganondorf's hands.
The scene where Ganondorf pummels poor young Link with his bare hands is just so unexpectedly brutal, given the art style, that it cements Ganondorf's badassery. Still, though Link is just a little kid, he is a little kid with a sword who has just bombed down Ganondorf's front door, smashed his way through an army of guards, and killed his pet. The humiliating part here is that Ganondorf still treats him like a child.
But it swings back around to awesome when you consider that yes, he treated Link like a child, but he was forced to do so PERSONALLY. Link disabled Ganon's two dragons (Helmaroc King permanently, and Phantom Ganon temporarily.) This nine year old child took out his base of operations, and forced him to deal with him himself, and that is definitely worthy of praise.
Just before the final battle, Ganondorf has an unconscious Tetra in his grip, and then zooms forward and beats down Link with his bare fists, knocking the Master Sword away, grabbing an utterly helpless Link, and forcing the pieces of the Triforce to unite so he can make his wish. That's not the awesome part. No, the person to get a crowning moment in this scene is King Daphnes, who shows up out of freaking nowhere and places his hand on the Triforce before Ganondorf can. And his wish? For the old kingdom of Hyrule to be washed away forever, along with Ganondorf. The King is willing to sacrifice his chance to revive his lost Kingdom just to deny Ganondorf his prize.
King Daphnes: Ganondorf! May you drown with Hyrule!!
To which Ganondorf lets out what is quite possibly the best villainous laugh ever shed in a Zelda game. It sounds like at that point, he has reached the point of clear insanity.
Even with its controversial art style, Wind Waker probably scored a lot of points with the end of the final boss battle where Link plunges his Master Sword RIGHT IN THE HEAD!
Not to mention he jumps ten feet into the air before sinking the sword into Ganondorf's skull and all this happens in a flooding arena. From the unarmed child beating, the unstoppable badassery of Ganondorf's health destroying sword slashes and unbeatable defense, to the insane laughter as he kneels on the floor, his head now being used as a swordholder... the battle is The crowning moment for Link and Ganondorf.
Even more awesome is the second version of this, which is rather hidden. Link does the behind-the-back parry, stunning Ganondorf, doing a 180, and then going for the "sword in the head" of Wind Waker fame. ALL IN ONE JUMP.
The above doubles as a CMoA for the developers, who were being rushed at this point in development. Most other developers would be short on ideas and would create a subpar ending, yet somehow, Nintendo produced an amazing ending to The Wind Waker that few had ever thought possible, what with the graphics style of the game. In fact, the ending was so good that Nintendo Power, Nintendo's official American magazine, called the ending one of the greatest endings on a Nintendo console of all time.
King of the Red Lions: ...You are surprisingly dim-witted.
How about just the fact that the Triforce appears in the first place? Only one other time did the holy relic appear in the entire series (Link to the Past), and that was in 2D and only in the final cutscenes. You enter the battle expecting nothing more than just a fun battle against the King of Evil. Then Ganon takes out Link and, after 400 years, finally realizes the dream that he narrowly missed out on in Ocarina of Time, reuniting the Triforce, which floats there, massive and glowing in all its holiness. The Triforce does little more than just float there before Daphnes makes his wish, the sight of the golden relic in all its 3D epicness is breathtaking.
The Shark Island secret cave. They pretty much send a freakin' army of Darknuts, Moblins, Wizrobes, Bokoblins, and Miniblins after you, and you still kick their asses. Once you are done, there will be tons of weapons lying on the ground as the remains of the slaughter. The best part? You can redo that battle as much as you want.
It's a very small Moment of Awesome, but ringing the bell at the top of the Tower of the Gods is probably the coolest and most original use of a grappling hook ever.
Ganon's Tower in this game gets major awesome points for being similar to, yet also different from the one in Ocarina of Time. It is built and placed not too far away from Hyrule Castle; as if Ganondorf is trying to make a point: his evil dream is still alive and the same. Probably the most awesome of all however, is when you first enter the tower to be greeted by that familiar music that was once played so menacingly on the organ years and years ago. Then the music fades as Link climbs the last set of stairs and stops completely when he reaches Ganon's door. It makes the heart sink into the stomach.
The cutscene that occurs when you enter said door is also pretty awesome. Ganondorf's speech about how pathetic and hopeless the world above the sea has become really affirms his wrath, and sets the mood for the upcoming battle. Then we have his transformation to Puppet Ganon which is just INTENSE.
The finishing blow on Ganondorf deserves special mention, but every time you use the parry attack is a CMOA. This Link is the most acrobatic yet, and the series' 3D entries only escalate from here on out.