It takes something really powerful to make people cry over something that died millions of years before they were born. This is one of those things.
The end of the Death of a Dynasty. The Tyrannosaurus rex mother became seriously crippled after trying to protect her offspring from an Ankylosaurus. We are then treated to a scene of the corpse of the mother T-rex and her two babies playing around it, unaware of their motherīs death. And then the meteor strikes and everything goes to hell, as expected . Sure, the scene where the T-rex babies and their mother are sucked into the incoming wind can slightly go into Narm territory, but the scene is still remarkably heartbreaking.
Earlier in the episode, there is a third baby T. rex who is constantly picked on by the other two. When there is no sign of it in later scenes, the narrator suggests it was eaten by its siblings.
The Walking with Dinosaurs Special about Big Al : Many people felt sad when the allosaur dies still young from his injuries and starvation.
The poor old Liopleurodon getting beached in Walking with Dinosaurs. This series is not kind to its older characters.
Before that, we have a brief shot of a dead Rhamphorynchus. The narration indicates that a lot of the pterosaurs died because the enormous winds of the monsoon jostled them about and shattered their bones. Poor things. It doesn't help that they were so dang cute.
The scene in Walking with Beasts when the Gastornis chick is eaten alive by ants is an odd mixture of this and Nightmare Fuel, just like the aforementioned cynodonts.
The mother Gastornis coming back to the nest and discovering that her baby is dead. Her reaction is to huff quietly then walk away. For a moment, you really feel sorry for this giant predatory flightless bird.
Also in Walking With Beasts, the mother bear dog whimpering while she digs her dead pups out of the collapsed den.
A fourth example from Beasts: the mother brontothere seen anxiously watching her dead calf. Especially heartbreaking is the fact that her brain is too small to even understand the concept of death, so she continues to guard the corpse of her baby and defend it from predators as though it were alive.
The entire Late Permian in Monsters is a slow journey to death for all creatures, since the infamous Permian/Triassic extinction is going to take place soon. And that was the worst mass extinction ever, the Cretaceous one coming only in second or third place : 90 % of marine and 70-80 % of terrestrial lifeforms went extinct.
In a meta sense, the eventual removal of the highly addicting Evolution Game (which accompanied Walking with Beasts) and later the Big Al game (which accompanied The Ballad of Big Al) from the franchise's website. Especially the latter, considering that it had been there for more than ten years. To make things worse, neither of these removals were announced beforehand.
The death of Bulldust in the 3D movie. One of the only scenes to be treated with any depth or gravitas.
What about what happens after Patchi loses in the duel against Scowler? Scowler has him pinned to the ground and under a tree and nastily tells him that he's no longer in the herd. When Juniper tries to help and asks why Scowler wasn't helping his brother, Scowler coldly insists "I haven't got a brother." This is enough to send Patchi into a Heroic BSOD, wanting to actually be eaten by the scavengers gathering around him.
There's also the implication Scowler's feeling guilty about this during Gorgon's attack, by how he's insisting Patchi to get to safety.