In one episode, Malcolm decides to hold everything in, becoming 100% agreeable. By the end of the episode, his internal monologue has become a screaming demonic voice, and he spits up a large amount of blood due to developing a severe ulcer.
Francis hunting down the mythical rat "Rose Marie" and instead ending up completely enveloped in her offspring. As funny as it is, you can't help thinking you'd scream like that too if you were trapped in a crawlspace and covered in live rats.
Craig's helper monkey going insane and trying to kill him and Hal.
Craig: He watches me while I pretend to be asleep.
The fact that this has happened in real life does not help.
Malcolm, Reese, Dewey, and Stevie being locked in a closed amusement park in the middle of the night then being chased by a crazed security guard.
Let's face it, the show runs into this trope very frequently. It comes with the Black Comedy.
Malcolm getting screamed at by his girlfriend's over-protective father when he finds out he isn't just her tutor. Malcolm is so terrified that he curls up into a fetal position.
In one episode where Lois is about to smash the TV to punish the boys for ruining her dress (which they didn't do), Lois finds out that they have hidden it while she wasn't looking. Then this happens...
Lois and her mother. Imagine being raised by people this cruel, manipulative and abusive, who simply do not care how horribly they damage their offspring. Lois' mother is actually WORSE than she is, but not by much. We can only hope that Malcolm never becomes President, because imagine what an individual that damaged would do with access to nuclear weapons.
Hal being covered in bees. Reese waking up in a room full of butterflies.
Malcolm and Dewey get stuck in a tiger enclosure at the zoo. The zoo workers briefly mention a similar situation in another zoo and how they're trying to figure out what went wrong with that one, and were going to try tranquilizing the tigers had Malcolm not pointed out that that would just tick them off long enough to kill them before they settled down.