- The scenes where Bastian discovers the truth about the lion Grograman, and sits with him so he won't be alone.
- Artax's death. And 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.
- 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.
- "ARTAX!" Every last second of that scene, as Artax sinks to his death, with Atreyu crying and begging him to move. The fade out following is absolutely heartwrenching.
- It's an in-universe example as well, since Bastian has to stop reading the book to wipe away his tears at this point.
- The "Big, good, strong hands" sequence.
Rockbiter: They look like big, good, strong hands, don't they? I always thought that's what they were. (sighs) My little friends... the little man with his racing-snail. The nighthob... even the stupid bat! I couldn't hold onto them... the Nothing pulled them right out of my hands. I failed... Listen. The Nothing will be here any minute. I will just sit here and let it take me away too. (Raises his hands again) They look like good. Strong. Hands... don't they.
- In the second movie, the scene showing Bastian's last memory with his dying mother.
- The extra heartbreak is that we see this memory because Bastian made a wish.
- Bastian wants to revive Atreyu (who he accidentally killed during a fight), but he only has two memories left at that point: his mother and his father. To save his friend, he has to sacrifice one of the memories and the implication is that he gets to choose which one to give up.
Atreyu: Your mother would've been proud.
- "Bastian, please...save us!" Whatever else can be said about the acting abilities of the child actors, Tami Stronach's delivery of this line is heart-wrenching.
- After Bastian reads about how Atreyu and Falkor begin searching for a human child to name the Childlike Empress.
"I wish they'd ask me. My mother had a beautiful name."
- The climax of the second movie has Bastion's absent father reading the book, realizing how much danger his son is in, and cheering his son on as he fights Xayide.
- Bastion's final wish is that Xayide had a heart, which causes her to cry over the evil she's done and disappear.