After Littlefoot's mother dies, Littlefoot is comforted by Rooter, an old dinosaur who Littlefoot runs into.
Rooter: Oh, it's not your fault. It's not your mother's fault. Now, you pay attention to old Rooter. It is nobody's fault. The great circle of life has begun. But see, not all of us arrive together at the end.
Littlefoot: What'll I do? I miss her so much.
Rooter: And you'll always miss her. But she'll always be with you, as long as you remember the things she taught you. In a way, you'll never be apart, for you are still part of each other.
At one point, a group of baby pteranodons are seen fighting over a cherry. When said cherry gets eaten by a lizard, their parent shows up and gives them an entire leaf full of cherries (one for each of them) and they all fly away together, presumably to go to the Great Valley. This is sweet (and funny) enough as it is, but the REALLY heartwarming moment is when the blue pteranodon sees a visibly upset Littlefoot lying on the ground nearby. What does he do? Offer to share his cherry with him! After arguing over a cherry with his brothers and sisters, the little guy is perfectly willing to share it with a complete stranger in an attempt to comfort him. Awww!
When all five main characters fall asleep together in a pile.
Littlefoot could let Cera smash her head in while trying to get her own food. Instead he grabs a handful, waits, and throws a portion down after she rams her head against a tree. He'd rather see her confidence boost than let her starve.
When they all finally made it to the great valley.
"We did it! We did it, together!"
Bonus points for the moment when Ducky introduces Spike to her siblings, who are all more than happy to accept him into their family.
That, and the part where all the kids are together again just before the end credits roll.
The Diana Ross' tune "If We Hold On Together", played over the closing credits. It not only sums up the movie's main premise, but is also a message to those watching it to never give up, no matter how hard life may become.
When the cold snap has made things very dire for the valley, the adults are discussing what to do now that their food has run out. The leader of the Stegosaur herd then appears and immediately announces he will take his herd out of the valley to help the natives conserve what they may have left. Even Mr. Threehorn is taken aback by this consideration, and even says nobody was saying they had to go. The Stegosaur leader doesn't budge, however, as he admits his kind eat more than the others do anyway. This earns him a respectful, warm farewell from the valley leaders.
Ducky finally manages to say she loves Spike after getting mad at him through over half the 8th movie.
Mr. Threehorn calling out Hip's father in the third movie. Especially Mr. Threehorn, since he's clearly reliving his own Heel Realization and apologizing to Cera when saying it.
The end of the The Big Freeze, where Mama Swimmer saves Spike from drowning in the icy water. If his cry of "Mama!" doesn't get you, the exchange that follows after ("You saved him!" "Of course I did, he's my boy") will.
Tricia's birth in movie twelve. She's just too cute...
Even more cute, she says her first word at the very end: Cera.
The prologue of the fourteenth film is heartwarming in and of itself considering the series has returned at all. It retells the events of the first film, released nearly thirty years ago, and also retells the ending of The Great Longneck Migration. It's a welcome trip down memory lane, and also outright mentions the death of Littlefoot's mother for the firs time since Migration (and out of universe, about thirteen years). It's a warm treat for longtime fans.
After taunting him the entire episode, once Chomper saves the day with his little arms in The Missing Fastwater Adventure Cera gives him a more good-natured tease along with a heartfelt "Good job, Chomper".