These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Ask anyone and they'd say Francis is the real main character of the show, not Malcolm, since he got the majority of the character development and became better off in the end.
Base Breaker: Every main character, especially Lois. Each character drifts from likable to completely insane. For the viewer, their mileage may vary on just how they're supposed to feel about anyone at any given time.
Broken Base: The Series Finale. Malcolm gets offered a lucrative job that would allow him to skip college and become rich. Lois and his family force him to pass up the job because in Lois' words "Malcolm needs to actually crawl and scrape" to actually be a good person. The big divide is whether people feel that Lois was actually right or if she was once more being a Control Freak.
Crosses the Line Twice: Domestic abuse, stalking, bullying, religion, death, infidelity, animal cruelty, incest, drug abuse, misogyny, racism; nothing is sacred, and it's all played for laughs. And, unlike shows like The Simpsons that try to temper some of the subject matter with heartwarming moments, this show hardly does it.
"Funny Aneurysm" Moment: Commandant Spengler's multiple amputations are continually played for laughs. His actor Daniel von Bargen would later lose a leg to diabetes, and attempted suicide when it looked like he might lose the other one.
Harsher in Hindsight: The man who tried to frame Hal for corporate espionage feared he was dying of cancer and wanted to clear his conscience, only to find out that he wasn't later. Paul Gleeson, who played him, died of cancer a year and a half later.
One has to wonder if Breaking Bad show creator Vince Gilligan looked to this show for inspiration, as this show has a lot of scenes and episode premises that become hilarious and/or eerie once you learn that the Bryan Cranston who plays Bumbling Dad Hal is the same one who plays morally gray, cancer-stricken chemistry teacher-turned-meth dealer, Walter White:
In "Malcolm Goes to College," Reese pretends to be a drug dealer in order to get the attention of a well-known (and cute) narc at school, culminating in Hal getting busted for possession of drugs, complete with a baby at the table, and Reese berating him for not telling him.
The episode "Reese's Party" centers on one of Francis's hoodlum friends breaking in and making crystal meth in the family's backyard (sadly, Hal is away with Lois at a bed and breakfast).
In another episode, Hal worries that he may have cancer and tries to hide it from his sons note (until he gets a call saying that the lump is benign), which is slightly better morally (but not as exciting entertainment-wise) than making meth with a high school drop-out to pay for the hospital bills and make sure his family has something to live on when he dies.
In "Jessica Stays Over," Hal obsesses over killing a bee. The Breaking Bad episode "Fly" was also about a Bryan Cranston character obsessing over killing a bug (in this case, it's a fly, and the reason is because the fly would cause adverse effects to the chemicals in the meth lab).
Similar to the above, is an episode where Hal is obsessed with gassing a colony of ants that have moved into the house. That episode, and the Breaking Bad episode both show a POV shot from the insect in question.
Another episode had him ask Malcolm (in a dark, serious tone) if he had what it took to do an upcoming task. When Malcolm responded yes, Hal, now cheerful, remarks "Great! We'll start tomorrow!" The conversation vaguely resembles the interactions between Hal and Jesse in Breaking Bad's first season, particularly the "Buy the RV, we start tomorrow" scene.
In "Reese vs. Stevie," a flashback of how he let his sons off the hook for one bad thing they did shows a bald Hal next to a burnt and smoking chemistry set. That moment doesn't get any more obvious in hindsight than this.
And then there's the time Hal paid two planes to skywrite a heart in the air for Lois's anniversary, only to have them crash mid-air. Flash-forward to Breaking Bad's second season finale...
On the episode "Malcolm Babysits," there's a scene where Hal is outside of a trailer in his underwear, which is how we first meet Walter White in the very first episode of Breaking Bad (only on the former, Lois was throwing him out; the latter was Walter trying to escape other drug dealers and the cops and recording a video will in case he gets shot or crashes his trailer).
(mixed with What Could Have Been): Aaron Paul (the actor best known on Breaking Bad as Jesse Pinkman) auditioned to play Francis (the older brother who was sent to military school), but lost out to Christopher Masterson (brother of Danny Masterson, who played Hyde on That 70s Show). If Aaron Paul did get the role of Francis, Breaking Bad would have been mistaken for a Darker and EdgierMalcolm in the Middle spin-off.
In the episode "Secret Boyfriend," Vicki (Malcolm's secret girlfriend) is dubbed "cheerleader scum" by Jessica. Pretty funny, considering that Jessica is played by Hayden Panettiere, who the following year would become thecheerleader, on Heroes.
One episode made a Godzilla parody by having Lois trash a city made of Legos. Come 2014, there would be a remake of Godzilla with Bryan Cranston in it.
Ho Yay: Hal and the father of a neighbor family, which is a Worthy Opponent for Hal's family at being a bunch of dysfunctional sociopaths.
Francis and Eric, especially during the Alaska arc. lampshaded by a bunkmate at one point, who tries to help set the mood with a harmonica.
Francis and Otto have a lot of moments. It's not too much of a stretch to assume Otto has feelings him.
Moral Event Horizon: Ida did many cruel things, but she definitely crosses the line when she drugs a man and forces him to marry her (then drugs her family after they find out what she's done).
When Stevie's mother left after he became independent. And she becomes a Karma Houdini whose completely forgiven by her Henpecked Husband and Steview when she rejoins the show.EvenLois,who has committed many heinous acts, called everyone out on the sheer wrongness of accepting a woman who abandoned her disabled child back into their lives due to how bad and selfish the sheer act was.
Lois and Hal's entire plan of making Malcolm's life completely miserable so he'll be "motivated" to become president.
Rooting for the Empire: Malcolm spends the night in a college, Lois goes along for her own creepy reasons. Cut to confrontation with the RA, who calls Lois out on the exact reason why she's obviously come with Malcolm and you realize that while he's a git, he's awesome at the same time. Even Malcolm doesn't know who to root for.
Malcolm's poison ivy reaction in "Company Picnic, Part 2".
Hal's fungal infection in "Hot Tub".
Unnecessary Makeover: Lois gets tastelessly made up in her workplace for being deemed untidy in her work report. With that, she can flirt her way to advantages, but she gets tired of it soon enough.
Wangst: Malcolm has some genuine reasons to be complaining or feeling annoyed/angered at his family - but at the same time, he sometimes feels unsympathetic because of how much he whines, complains... he even gets called out on this in one episode.
This became a deliberate part of his character after a few seasons, with him becoming an Emo Teen.
Francis. Sometimes it seems he complains about everything. Even things that have nothing to do with his mother.
The Woobie: You could call every character on the show this trope, after all "life is unfair".
Jerkass Woobie: This applies to everyone the rest of the time. Bad things never really stop happening to the family, so whether they're this or a regular Woobie comes down to whether or not they deserve what's happening to them in a given episode.
Occasionally, a character would purposefully play themselves up as this to get something.
What an Idiot: In the second to last episode, a girl pays him to take her to the prom. He turns out to be quite charming and she starts to develop feelings for him, wanting to spend the night with him. If it were any other guy, they would have gone to the middle of the football field and had sex, but instead Reese realizes it's midnight, and she only paid to be with him until midnight, so Reese admits he faked his charm to keep his "customer" happy, and leaves her behind.