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.
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.
Commendant 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.
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.
Given all the scenes or episodes that unintentionally mirror Breaking Bad (which also stars Bryan Cranston), one has to wonder if Vince Gilligan looked to this show for inspiration.
In the episode "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. This culminates 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 (until he gets a call saying that the lump is benign).
In "Jessica Stays Over," Hal obsesses over killing a bee. This becomes even funnier when you see the Breaking Bad episode "Fly" where Walt obsesses over killing a fly.
In "Reese vs. Stevie," a flashback shows a bald Hal next to Malcolm's chemistry set. Wow, where else have we seen a bald Bryan Cranston next to a chemistry set?
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...
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.
Ho Yay: Hal and the father of a neighbour family, which is a Worthy Opponent for Hal's family at sociopathy.
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).
Reese crossed it in "Funeral," when he decided to break Dewey's birthday present and then bury it with their late Aunt Helen.
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.
Some Anvils Need to Be Dropped: In "Billboard", the three boys sneak onto a billboard advertising a strip club to deface it. When they're caught, Malcolm tricks everyone into thinking it's a feminist protest. It starts out as a cynical parody of women's rights activism—but then the entire situation gives Reese an epiphany, and he ends up giving a heartfelt, honest speech about how women just want to be listened to and treated like normal people. Pretty impressive, considering he earlier called the protesters dogs who secretly wanted to be strippers.
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.