Littlefoot's mother's death. She fights a LETHAL predator to protect not only her son, but Cera as well. She gets a fatal wound in the process, but still stays on her feet long enough to save them and get them to (relative) safety as an earthquake starts. Then when she had succumbed to her injuries, her last words to her son are to head to the Great Valley and that she'll always be with him. He then watched as she finally died. The kicker? The end of the scene is pulled off with the camera pulling back, so that you can only see the outlines of the two characters against the darkness... you don't even realize she has died until you hear Littlefoot speaking to her and getting no response.
Another moment that counts is when Littlefoot sees his shadow cast large on the side of a cliff, and mistakes it for his mother. Because you know she's dead, but he doesn't understand, and he's so sure she's back, he's so happy but you know better and you have to watch him, knowing what's coming...
Made even worse when he licks the rock.
The scene after Littlefoot meets Rooter. He's wandering aimlessly, and nuzzles his head against the ground while sobbing always gives me a lump in my throat.
The scene where the little pterodactyl tries to cheer Littlefoot up with food and Little Foot just stares dully, not even reacting...
The part where Littlefoot's mother appears to him in the form of the clouds. As he tries telling her he tried and failed to find the Great Valley, her form seems to start departing.
"Mother? Mother? Don't go mother! Don't go!" Geez...
The song "If We Hold On Together". Also the dialogue that comes before it; "And they all grew up together in the valley, generation upon generation, each passing on to the next. The tale of their ancestor's journey to the valley long ago. "
Here's the cover with the kids who played Cera and Ducky, Anndi McAfee and Aria Noelle Curzon respectively, singing it.
The movie is made a thousand times more heart-wrenching when you discover what happened to Ducky's voice actress, Judith Barsi, a few months before the movie was released. (Warning: do not click that link unless you want a bigger Tear Jerker than all these examples combined.)
The ending to Journey to Big Water(Mo just didn't want to leave his new friends) and the song "No One Has To Be Alone" (especially the end credits version). To some, even scenes from a sequel (or even a song from said sequel) can be tearjearking.
"Family" in The Big Freeze.
" Always There" from the fifth movie.
The final verse of "On Your Own" (From The Secret of Saurus Rock), and the entirety of "Bestest Friends" (From the end of The great Longneck Migration)
In fact, the ending of "The Great Longneck Migration". Littlefoot's distress at having to choose between his friends and grandparents, or his long-lost father. And his final explanation to his father that he just isn't ready to leave his friends and grandparents, despite really wanting to go live with his father.
Littlefoot's initial reaction to meeting his dad. We expect a joyous reunion, instead Reality Ensues and Littlefoot runs off with tears in his eyes and feelings of betrayal in his brain. He gets over it, but still...ouch.
Rooter comforting Littlefoot after his mother dies - he's initially gruff, but then when he realizes why Littlefoot is really so upset, tells Littlefoot that he'll always miss his mother, but she'll always be a part of him as long as he remembers what she taught him.
Particularly the line: "It's nobody's fault." It's such a sweet line in its own right, showing the compassion an old dinosaur has for a heartbroken child (and hints that he's been in Littlefoot's place). However, if you've ever lost someone important, then you'll know how desperately you try to look for someone to blame for their passing, including yourself, and sometimes you really need to hear someone say that to you.
But even after that, the fact that he doesn't really try to help Littlefoot at all, but just leaves him there. Excusable, however, due to the fact that he was a character created at the last minute to soften the blow the death scene had.