I'm gonna have to echo what the previous few people said and go with Littlefoot watching his mother die. As I mentioned in my introduction post in the Welcome Center, I cried when I saw that part again for the first time in over 15 years.
Other honourable mentions:
- Pretty much everything that follows the aforementioned scene. When that little pterosaur tries to cheer Littlefoot up by giving him the cherry, and keeps nudging it closer and closer. Littlefoot just stares on lifelessly and doesn't even react, and then the pterosaur's eager smile falls away. And then Littlefoot seeing what he thinks is his mother's shadow on the side of the cliff. Even the scene with Rooter, even though Rooter is trying to comfort Littlefoot, is still kinda sad in its own way. "The great circle of life has begun. But see, not all of us arrive together at the end."
- Littlefoot and Cera's fight. Quoting WeirdRaptor from page 2, who described it best: "The scene when Cera insults Littlefoot's mother... when you saw the rage Cera's hurtful words envoked in Littlefoot. One part of you knows that Littlefoot is better than that while the other half is egging him on to rip her head off. Very emotional."
- After the other kids rescue Cera from the predators and prank her with the tar, and then she leaves them in tears. Granted, I do feel Cera kinda got what she deserved. Still, she's just been through a traumatizing experience, and subsequently gets laughed at and utterly humiliated by her friends, and it's enough to make a normally tough and headstrong dinosaur like her completely break down. It's the moment when she seems to realize how awful she's been, and despite all her bravado, she's forced to come to terms with the fact that Littlefoot is a far better leader than her.