The opening to Cruel Sea is probably the most memorable moment of the entire series, when Branagh narrates "The predator is laying in wait for its prey, waiting to strike," with a Eustreptospondylus peering into the ocean expectantly - when suddenly a giant Liopleurodon leaps out of the water, snatching the large theropod off the land for a tasty meal. The episode title card, "Cruel Sea", punctuates the moment.
Nigel Marven tagging the giant shark Megalodon in Sea Monsters.
The mother Dimetrodon defending her nest from the rival female in Walking with Monsters.
Another example from the same program: the tiny predator Euparkeria becoming a gigantic Allosaurus and frightening the croc-like chasmatosaur which chased it just before (like saying: "Ah, what are you going to do now?")
The ending of the WWD episode New Blood, when a herd of Plateosaurus march in, scaring off the Coelophysis.