"I love that nothing in my life is complete till I've shared it with you."
"You look me in the eye, and you tell me you can't do it."
When Ida actually jumps into the street and loses her leg to save Dewey.
"Malcolm, I'm an average guy, in the middle of my life, in a job that can replace me in an hour. I was never an important man. You're the only important thing I've ever done."
The episode where the boys all unite to get revenge on Hal's family for reducing Lois to tears, her transgression being simply to exist and yet repeatedly suffering Kick the Dog moments whenever she genuinely tried to be nice to them.
Even more heartwarming than that. After seeing their mother reduced to tears, without any hesistation at all, the boys simultaneously get up and proceed to enact their Roaring Rampage of Revenge, which they conduct in complete silence and wearing looks of utmost serenity. It's safe to say, they got the message across that you do NOT mess with Lois!
A smaller moment at the end, when Lois — who's spent the entire episode, not to mention their entire relationship, being equally hostile to Piama — considerately asks her if she's comfortable during the drive back. Everyone in the car catches it without saying a thing.
The episode where Reese and Malcolm are tricked into believing the other is gay, and in an attempt to prove their acceptance, they're nice to each other for a change. This even leads to them dancing to an ABBA song together in one amazing moment. Like many heartwarming moments, it also doubles a funny one, too: Malcolm and Reese each wear an extremely uncomfortable rictus grin as they pretend to like and dance a song they both hate to humor one another, but then they start getting into it. Really getting into it, to the point that the rest of the family has to stop and stare in confusion, surprise and —in Dewey's case— maniacal glee.
The episode where Lois, who had increasingly grown stress at the boys ruin a trip to the mall, as well as her own fantasies of having daughters instead of sons begins to crumble, ends with all of them including Hal giving Lois gifts in their own way to show that they care about her.
After discovering that Hal and Lois have absolutely no photos of Dewey growing up, he takes Hal's wallet and puts the two on an elaborate scavenger hunt to get it back. Along the way they have to pick up party supplies from the people who've got the contents of Hal's wallet (who also take the opportunity to mock the two for how they've treated Dewey). Eventually, they find Dewey at a video arcade he's paid to keep open after hours. Hal and Lois assume he wants them to throw a party just for him. But it's not, it's for Jamie, who's there with a babysitter. Dewey accepts that Hal and Lois neglected him, but he's not going to let Jamie go through the same thing, and has provided them an opportunity to shower Jamie with attention. Lois even consents that what Dewey has done is an incredibly nice thing for his brother... before telling him that everything he eats after the party will be soaked in sardine juice.
The episode where Lois loses confidence in her mothering abilities, and the flashback with her attempt at parenting Francis as a toddler (An Enfant Terrible one at that) was pretty heartwarming, especially compared to their regular interactions. She catches him as he's trying to set a teddy, doused in lighter fluid on fire, takes it and holds it in the fireplace. Then she turns on the flame, still holding her hand in the fire, and gives a speech to the toddler about how she'll do anything to keep him safe - even if it means having him hate her later.
After fighting with her sister and acting childish and crazy the whole episode, Lois learns that Susan has a fatal kidney disease. Lois then undergoes surgery and gives up her own kidney to save her.
And when Susan accuses Lois of never loving her, Lois gives this speech.
When Lois finds out that she is pregnant with Jamie, it is at an awful time; Ida injured herself outside their house and is suing them over it, when they're already horribly in debt. When Malcolm, Reese and Dewey find out about the pregnancy, they get angry and storm upstairs. While Lois is still having to deal with Ida, they come back down, and, having had a change of heart, tell her they don't mind sharing their stuff with the baby.
The episode where Hal visits Francis in military school. Hal is disappointed that Francis hasn't achieved anything during his stay and gets the impression that Francis was nothing but a trouble maker. Francis then criticizes Spengler for yelling at a fellow cadet simply for hugging his father goodbye. Spengler uses this to explain Hal that Francis was always trying to challenge his authority. Hal then realizes that even though Francis doesn't have any awards, he found another reason to be proud of him.
At the end of a late night of looking at their finances and trying to write a will, Hal and Lois concede that they're terrible parents and the latter even breaks down in tears about it. As if on cue, there's a loud noise in the boys' room and Dewey emerges with an arm injury. The parents promptly and lovingly attend to their injured son as Hal rushes out of the house to take him to the hospital. Lois, alone, ironically echoes her belief that they're terrible parents.
I don't think that this description does justice to that scene. After he rushes down to them, they morph into a perfect team of perfect parents, distracting Dewey from the pain with math while checking his eye movements. They immediately decide to drive to the hospital and know exactly which one: One is preferred for their child-accidents but they know that the doctor they consider most competent is absent (which shows that they keep track of such kind of information). While they carry Dewey out, he asks for some apple juice but it turns out they only have orange juice at the moment (or the other way round). It is only then that Lois breaks out of that perfect "kid-in-emergency"-routine to note: "Of course we don't have apple juice - we're such terrible parents".
After failing music class, Malcolm reluctantly seeks tutoring from Dewey. After trying and failing to teach him, Dewey gets frustrated and tells Malcolm that he simply has no appreciation for music. This leads Malcolm to take revenge with a prank that leaves them both temporarily deaf. A few days later, Malcolm wakes up and, after turning on a classical music CD, joyously realises that his hearing is back. The episode ends with Malcolm listening to the music with a deeply thoughtful look on his face.
Early in the series, Malcolm's class is having a sort of fair, where each of his peers display a talent. Malcolm hides his when his family shows up, until the fair starts to fail. He goes onto a stage to show his talent, which is an absolutely absurd ability to calculate large numbers very quickly, like the product of 2 credit card number times 9 squared, in as long as it takes to read that equation. After this goes on for about a minute, we cut to a scene in the car, driving home. It's silent, Malcolm feels like his family thinks he's a freak. After Dewey asks if he's a robot, and Hal telling him Malcolm is just very very very smart, Francis makes a joke, shortly followed by a few more, and everyone laughing.
Reese: Hey! Analyze my lunch, buttface! *burps in his face*
This moment really has even more of an impact when you see Hal and Lois' faces during the math scene, where they have a look of intense discomfort about how their son is much smarter than them.
"Red Dress" has a strange platonic one that doesn't even involve a main character. It's oddly moving how Hal spent his anniversary befriending the unnamed bathroom attendant who was happy that someone made eye contact for once, and by the end of the night they're sharing the meal that was meant for Lois, over a copious amount of alchohol and hearty laughter. It's only mildly ruined when you find out it was Hal who burnt the red dress and ruined the evening for everyone else.
In "Malcolm Defends Reese", Malcolm needs almost zero deliberation before he decides to purposely tank his grades to get Mr. Herkabee to stop torturing Reese in front of the class — even after Reese responds to Malcolm's offer of sympathy by splitting his lip open. The fact that his decision is never commented on or acknowledged as a big deal is what makes it particularly heartwarming, as is the scene at the end where only a blink-and-you'll-miss it glance between the two brothers, no big confrontation or declaration of gratitude, implies that Reese knew what Malcolm did for him and that his pummeling Herkabee with the dodgeball was for Malcolm's benefit as well as his own.
"Watching the Baby," by the end of the episode, Reese sacrifices a chance of attending Prom with a beautiful girl just because he found out Jamie didn't have his binky and scurries back home just for Jamie.
At the end of "Softball," Lois concludes that Malcolm is acting out because of the new baby and promises to spend time with him one-on-one. Malcolm's "Thanks, Mom" is dubbed by his younger voice.
In the series finale, Reese and Grandma Ida have surprisingly heartwarming moments as they plan out the 30-day mess to keep Reese on as a full-time janitor. She even calls him a good kid, and he says he loves her. It should also be noted that in Ida's first episode along with Victor, they hated everyone except Reese.