The scenes where Bastian discovers the truth about the lion Grograman, and sits with him so he won't be alone.
Artax's death is arguably sadder in the literary version, as he's a Talking Animal here and as such his bond with Atreyu is more properly fleshed out. He knows he'll die, but he can't find it in his heart to resist. So he tells Atreyu to let go and stop trying to save him so he won't drown too, then gently tells him to look away so he won't have to see him go under. Atreyu does, crying the entire time. (This is a tearjerker in-story; Bastian cries while reading this part.)
"I can't stand the sadness anymore," cries the little horse. "I want to die!"
The ending, in which Atreyu and Falkor make up and part with Bastian and set out to tie up the story's loose ends.
As nasty as he was, G'mork seemed genuinely hurt by the dark princess's betrayal, even more so than being left chained and starving. It doesn't help that he was falling in love with her and was gladly received by her and her kingdom - remarking that nobody had ever treated him so kindly before; if only he had found Spook City before spitefully taking on his mission to destroy Fantastica, he might have realized that there was a place for him to call home after all.
