In the first film:
"Stuart Little gets scratched tonight!"
- The scene where Stuart gets trapped in the washing machine and nearly drowns. Thankfully, Mrs. Little saved him.
- During the boat race scene where George's rival Anton was willing to sink Stuart's boat just to win the race... with Stuart on board.
- Smokey and his band of gangster alley-cats are quite menacing, especially to a little mouse like Stuart. At first they didn't plan to kill him but rather have a mouse family, the Stouts, adopt and take him away from the Littles. But when the plan backfired (due to the Littles finding out Stuart's real parents died in an accident years ago), killing and eating him was Plan B.
- Stuart's biological parents' deaths: they were shopping for groceries when an unstable pyramid of cream of mushroom soup cans start to fall and spill and their bodies were so destroyed that their dental records were called to identify them. Think about this: for a human, a spill of creamy soup is a messy inconvenience while for small rodents, it could be an avalanche of heavy canisters of liquid that could flatten them.
- The photos the police show the Littles when they discuss the potential fate of Stuart after he has been kidnapped by the Stouts. Whatever was in those photos, they were not for the faint of heart.
In the second film:
- If you thought Smokey was bad, the Falcon is ten times worse. He is a lot more malicious and cruel and almost succeeds in killing both Stuart and Snowbell. James Woods' performance especially helps build up Falcon's creepiness.
- The scene where Stuart goes down the kitchen sink to retrieve Mrs. Little's ring (which, in reality, was stolen by Margalo) only for the string he was holding on to snap and nearly falling down the hole. Good thing Margalo saved him in time.
In the animated series:
- Falcon returns in the episode "A Little Bit Country" where he plots revenge against Stuart (as well as Snowbell and Monty for revealing Falcon's return) with an army of crows. Though he is a bit tamer and goofier compared to the film, he still has dark intentions to kill those he wants.
- The raccoons in the episode "The Great Outdoors" who start out as little more than comedic villains, but gradually become more menacing when confronted with Snowbell. After Snowbell refuses to let them steal the Littles' food they threaten to pluck his fur. When you consider that, in real life, raccoons have been known to prey on domestic cats its all the more frightening.
- The episode "A Little Vacation" where the Little family stay at a country inn for the night (after getting confusing directions from Uncle Crenshaw) which claims to be haunted by a ghost, which leads to a lot of spooky and creepy moments. It turns out that it was only a story made up by the Inn Keeper but we do not know that until the end of the episode...