The movie does a pretty good job of making a cute little goldfinch and its chicks absolutely terrifying. See Family Unfriendly Death.
Hopper in his first appearance, and some appearances afterwards. Especially the scene where he kills a few of his henchmen with a bored look on his face.
Hopper when he's attempting to strangle Flik: "I'll get more grasshoppers and be back next season. But you won't!!!"
Hopper menacingly approaching Flik, fire burning in the background, with the greatest murder-face on a family movie villain.
The theme park attraction at Disney World, It's Tough To Be A Bug.
This movie manages to make a rainstorm pretty terrifying. After all, normal raindrops hit the ground like watery napalm.
The entire sequence at the end of the movie, beginning with the rain. What is a normal and perfectly harmless occurrence for we humans is amplified into a nightmarish and regular disaster for all bug kind. Amidst the chaos, Hopper still manages to spot Flik, snatch him, and fly off. Flik's friends from the circus try to come to the rescue, but their rescue attempts are all foiled. (Admittedly, the incident where Hopper lost one of his antennae helped to alleviate this troper's fear at a young age.) Not even Princess Atta can keep Hopper away for too long, and his final death, albeit very karmic, in and of itself was very unsettling.