Base-Breaking Character: 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 who refuses to accept responsibility for her lot in life.
Easily Forgiven: Lois calls out Kitty for abandoning her family, leaving them destroyed, and then returning after she'd done everything she wanted and expected a simple apology would do. After Hal tells her that it's expected to forgive the love of your life for absolutely anything, Lois, who rarely apologizes for anything, apologizes to Kitty, with Kitty never having to do any real atonement.
Reese tends to be the most popular of the brothers, as he gets a lot of hilarious lines from being the dumbest of the brothers, as well as his secret talent for cooking.
"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 Visits 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 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).
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.
(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 could have been mistaken for a Darker and EdgierMalcolm in the Middle spin-off.
Hal's father is named Walter.
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 the cheerleader, 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.
Francis and Otto have a lot of moments. It's not too much of a stretch to assume Otto has feelings him.
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.
Craig. He may be a dick a lot of the time, he still doesn't deserve all of the nightmarish things he endures that would make Franz Kafka proud.
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. Even Lois, 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.
In the same season, there was Lois, Hal, and Dewey planning on spending a check made out for Malcolm (that Malcolm didn't know about) worth $10,000 with the intention of eventually paying the money back to him. Hal wants to buy a boat, Dewey wants a Rolex, and Lois wants the pipes fixed, but after initially planning on giving the money back to Malcolm, she caves and blows all of it on an antique dollhouse (that promptly bursts into flames when she demonstrates it to the others). They only recover a third of the amount to give back to an unaware Malcolm with no word on if they will ever fully repay him. This becomes even Harsher in Hindsight when financial problems come up in the finale as Malcolm needs more money to afford college.
Reese, Dewey, and Malcolm in "Hal Grieves." Hal's father dies and Hal, instead of grieving, fears that his sons won't remember him fondly just as he didn't remember his father fondly and throws himself into bonding with his sons. Reese, Dewey, and eventually Malcolm all decide to manipulate him into spending a lot of money on whatever they want, essentially buying their love; Malcolm even tries to get Hal to buy him a sports car. Fortunately Lois, the only one concerned about Hal's well-being and grieving process, intercepts and promises to make the boys suffer.
In the finale, it is revealed that the boys crossed this way before the series even began when they tricked Lois into thinking that she was dying of cancer so she would be too grief-stricken to notice that their report cards that they asked her to sign were terrible. They themselves acknowledge it as the worst thing that they ever did.
Herkabe crosses this in Malcolm Films Reese. he manipulates Malcolm into filming Reese's inner thoughts simply to humiliate them both.
Cameron Monaghan, well-known for playing Ian Gallagher on Shameless, appears here in an early role as one of Dewey's "disturbed" classmates. Coincidentally, Emy Coligado would go on to appear in Shameless for an episode as a social worker.
Alanna Masterson, sister of Christopher Masterson (Francis), appears in Malcolm's Money; she'd go on to achieve wide recognition as Tara in The Walking Dead.
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.
The Scrappy: Jessica isn't the most popular character due to her constant Jerk Ass behavior and absurdly easy manipulation of the brothers, outwitting Malcolm multiple times even when it doesn't make sense for him to fall for it, and overall being a Karma Houdini with a only a Freudian ExcuseRunning Gag as an excuse.
Some Anvils Need to Be Dropped: "If Boys Were Girls" teaches that the gender of your baby does not make them easier to deal with or that they'll behave better than if they were the other gender. Even today, many people still don't recognize this.
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.
Values Dissonance: A Season 1 episode has Lois being told by another student's parent that Malcolm has been throwing around "the R word," which is meant to be a joke about Political Correctness Gone Mad. Now that the word "retarded" has crossed the line to being considered offensive, it comes off rather differently, especially with Malcolm being the Insufferable Genius that he is.
In a real way, the entire show and its concept. When it launched, it still got some flack for "not being very funny" due to the legitimate sociopathy and abusive behavior of much of the cast, but many people rolled with it as absurdist humor. Come The New '10s, with a much greater general understanding of the kind of psychological damage emotional abuse inflicts on children, a lot of the relationships of the show seem a lot darker and unfunnier, though it still tends to come off as an absurdist, extremist portrayal of sibling and family relationships.
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".