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Some of the scenes involving Gerry and Jess discussing family matters can be quite saddening to watch. At one point while Gerry's scolding his daughter, Jess brings up his Disappeared Dad tendencies, and he's obviously upset by it.
Oscar's Heroic Sacrifice. Especially how anguished his partner becomes at the sight, knowing there's nothing he can do about it.
One of the death scenes late in the game, which happens when the group reaches a dead end while the Troodon are chasing them. As they're surrounded with no way out, Gerry and Jess realize that it's the end, close their eyes, and hold each other tight.
Nima's death scene, especially if you listened to her entire Back Story near the end.
D-Caf's body, or whats left of it at least.
In the worst possible ending for the game, Jess will be the Sole Survivor of the entire group. The final scene ends with her being all alone on the escape boat, quietly weeping after having witness the death of her father at the jaws of the Tyrannosaur.