The female Triceratops that fights off the Tyrannosaurus in "T-Rex Returns" in order to save the baby Triceratops that was being attacked.
Nigel acquires baby Theo by saving him from a Tyrannosaurus.
The female mammoth is wounded by primitive human hunters in "A Mammoth Undertaking". Despite this she accepts and befriends modern human Nigel and follows him to the modern-day park.
Another example is the same mammoth being accepted by the African elephants' matriarch after risking to "die for loneliness" due to refusing to eat any food.
That example is even cooler when reading the behind the scenes about it. They made a giant puppet of a mammoth head, then animated it in front of the elephant. They weren't sure how she'd react, but to their surprise the elephant interacted with it and welcomed it as it would for a real elephant.
Nigel's Microraptor befriending his pet macaw in "Dino Birds".
Nigel watching the pterosaurs as they fly and hunt.
Near the end of "Saving the Sabretooth", the last two Ornithomimus eggs hatch, and the babies imprint on Bob.
Everyone working their hardest to save Terence after Matilda had nearly killed him in "A Bug House".
In "Supercroc", Nigel encounters two juvenile Parasaurolophus when they happen upon his jeep and they take a moment to investigate it.