The climax halfway through the book, when Bastian finally calls out the Childlike Empress's new name.
When Bastian uses Al Tsahir at the top of the Star Cloister.
But if he speaks my name a second time From the end to the beginning I will glow in one moment With the light of a hundred years
Comes at a pretty high price, though, as it means that since he's used up all Al Tsahir's light, he no longer has it when he really needs it. The irony isn't lost on him, especially since the entire scene at the Star Cloister, while impressive (and gives a few Fantasticans a momentary glimpse of the real world), was basically just another instance of Bastian showing off and ultimately didn't accomplish anything of any worth.
Atreyu's meeting with Gmork, while less dramatic than in the film, still counts as pretty awesome, especially when G'mork at the end of the scene realizes just who it is he's spent the last half-hour talking to and basically laughs himself to death over the irony.
The fight between Bastian and Atreyu at the Battle for the Ivory Tower.
The Ivory Tower is pretty much this all by itself; the accompanying song just adds to its majesty.
Falcor making his big entrance by rescuing Atreyu just as he's about to sink.
Atreyu's bravery when faced with the Great Stone Gateway. He's just seen a knight get vaporized trying to make it through. As he considers what to do, there's a long close-up on his face, as we see his fear slowly change to determination. And then... "I'm going to try it."
Also, Bastian shouting encouragement. "Be confident, Atreyu! BE CONFIDENT!"
Atreyu's ride on Falcor.
Atreyu killing G'mork. "If we're about to die anyway, I'd rather die fighting! Come for me, G'mork! I am Atreyu!"
"I will not die easily. I am a warrior."
Bastian calling out his name for the Empress.
Bastian giving the bullies their comeuppance with Falcor's help.
The look on his face when the Empress asks him to make a wish. He thinks for a moment... and then he looks up with this badass smile that tells us exactly what he has in mind.
The second film may be cheesy, but Bastian's defeat of Xayide is still awesome. "I wish you had a heart."