After the end credits of Finding Nemo, an angler fish approaches a tiny fish... which then opens its jaws wide enough to swallow the angler in one gulp.
The title character in Riki Tiki Tavi. Awww... he's so cute and fuzzy... HOLY SHIT LOOK WHAT HE DID TO THAT COBRA! However, Riki Tiki Tavi isn't malevolent. He's actually trying to kill the cobras because they're harming the humans, so this is a more traditional example of Reptiles Are Abhorrent and possibly also What Measure Is a Non-Cute?. He does display slight sociopathic tendencies; it was justified to kill the cobra and his eggs to protect his owner, but it is a little dark to outright gloat about it to his widow's face (especially since preserving her family was the whole point of their attack). Then again, the taunt is as much about drawing her away from the human family as anything else.
"And Nag was dead before the big man blew him up! I killed Nag! Come and fight with me, Nagaina!"
The rabbit in the 2010 film The Illusionist likes to bite people and snarls like a raving monster, though isn't as deadly and terrible as it believes it is.
Kung Fu Panda 2: Lord Shen. He's a peacock, not something you'd expect to be a villain, but he is a genocidal would-be conqueror eager to kill anyone standing in his way and he is terrifying in personal combat.
Ice Age: Continental Drift gives us Squint, a pirate rabbit.
In Hoodwinked, Boingo is a pink rabbit who is also the Goody Bandit. He's implied to be an Easter Bunny given that he writes a map on such an egg.
Momotaro's Sea Eagles and its sequel Momotaro's Divine Sea Warriors are military propaganda films made by Imperial Japan during World War II. They're targeted towards children, so the main characters are mostly adorable cartoon animals. The climaxes of both films involve said animals shooting, stabbing, and bayoneting Caucasian-looking, English-speaking demons. When you think about how real-life Japanese forces behaved during World War II, it becomes even more chilling.
Epic: Small creatures like mice for the Leafmen and presumably others like them. Also chipmunks, apparently.