When Manny is telling the kids a story that ends with a "big happy family living happily ever after" one of the kids ask him where is his big happy family, which almost makes Manny break in tears before Diego scares the kids off in response.
Young Ellie's flashback; a lost Mammoth calf all alone in a blizzard, losing all hope until Crash and Eddie's mom finds her and takes her in, notably its remembering this moment that makes her realize that she is a mammoth and not a possum.
A Genius Bonus for wildlife buffs - Opossums give birth to many, many babies - and the reason they seem to have six at a time is that most infants don't reach a teat in time. For Ellie's possum mom to only have Crash and Eddie left when they met, means something tragic must have happened to her litter. From a maternal point of view it explains her taking in Ellie.
Scrat's Disney Death. Sure, he gets better, but for those who watch the films mainly because of him, it's sure to be one of the biggest.
Manny trying to tell Ellie how he feels, but he decides to let her go due to his dark past. Bonus points for John Powell's musical score during the scene.
When you think about it, Cretaceous and Maelstrom are Tragic Monsters. Yes, they tried to eat our protagonists (and Scrat in the video game), but both creatures were from the Mesozoic era (a geological era that ended 65 million years before the events of the series) and have been cryogenically frozen for god knows how long, only to wake up in what for them is an alien world, alone with only each other for company. Considering that we don't see any Ichthyosaurs / Metriorhynchus and Pliosaurs in Dawn of the Dinosaurs or Buck Wild, the may as well be the Last Of Their Kinds. Cruelly ironic considering that it's one of the main characters (namely, Manny) who spends most of the movie believing he's the Last of His Kind when it's revealed in the end to be further than the truth, while the main predators hunting him and his friends are very likely the endlings of their species.
It doesn't help that both characters are The Voiceless. For all we know, they could just be scared animals having just woken up after being cryogenically frozen long after their species should've gone extinct. With this in mind, Manny luring them to their deaths in order to free Ellie may very well be a Mercy Kill.
When Diego asks Manny what's holding him back from being with Ellie. Manny's response? "My family".
Manny letting Ellie go due to his Dark and Troubled Past and looking at his reflection in a puddle. Sure, he and Ellie end up together, but it's still truly a tearjerking scene.
When Manny looks into the pond at his reflection, lamenting about being the last mammoth.
