- The Reveal of the Secret Test in "Command Crisis", where the team hears a recording of Skipper praising their strengths and talking about how he wanted to make certain they could handle themselves if something ever happened to him.
- The ending of "Cute-astrophe". When Alice finds the caged penguins and announces that they'll finally be out of her hair because they're being shipped to Copenhagen, all the zoo patrons protest, forcing her to concede and let them stay.
- The penguins getting all teary-eyed over having to let Eggy go, and wondering if he'll remember them. At the end, Eggy repeats Skipper's catch phrase, "Cute and cuddly, boys!"
- A blink-and-you-miss-it example from the same episode would be Skipper's expression when Private starts giving his own plan of action.
- "I Was a Penguin Zombie". The premise of the episode was that Skipper got a broken wing, and in an attempt to escape the hospital room, triggers a series of events that make Skipper look like a zombie, and the others jump to the wrong conclusion and run away, with Skipper chasing after them each time he finds them until they start trying to kidnap him (they want to see if they can cure him) in a very painful manner (thanks to the muscle-numbing cream severely limiting his speech, he can't tell them otherwise). The ending, the effects of the cream finally wearing off and Skipper finally convincing everyone he's not a zombie is what earns it a place on this list.
- "An Elephant Never Forgets"."But he always forgives."
- Skipper doesn't want a shot, so he hides. To get Skipper out of trouble, Private volunteers to take his shot. Skipper sees it and then finds out through Mason and Phil that Private could get really sick (or worse) from getting two shots in one day... so Skipper decides to simply suck it up and get the shot.
- Also, after Skipper switches places with Private, just before Private leaves, he assures Skipper that they won't think any less of him just because he's scared about getting a shot.
- The ending of "When the Chips Are Down", especially this image.
- Julian going Papa Wolf to save the baby Fossa (a species that usually eats lemurs) once he finds out that it sees him as its dad. Full details are on the Awesome page.
- In "Jungle Law", Julien's Incompetent Leadership during a blackout causes the entire zoo to descend into chaos. When the whole mess starts, Skipper swears he'll tell Julien "I Told You So" before gathering the Penguins, Marlene, and Maurice to quell the riot. Afterwards, when everything has calmed down and the zoo is determined to punish Julien, Skipper, instead of saying "I Told You So", claims that everything worked as Julien planned it, as the riot was intended to keep everyone's mind off the blackout. Julien is released unharmed, and the zoo rushes off to celebrate. Cue a proud smile for Skipper from Marlene, and Private declaring the act to be the most noble thing he's ever seen.
- "Operation: Antartica" is one where we get Private friendship with Hunter a Leopard Seal (a carnivorous species that eat penguins), they were able to stay this even though the other penguins and the leopard seal scoff at this. With Hunter even saving Skipper, Kowalski and Rico from getting eating and Private saving Hunter dad.
- The ending of "Kaboom and Kabust". Kowalski comes up with an idea to calm a more-psychotic-than-usual Rico by trapping him in a bouncy castle used to absorb his behavior, and the plan works! Rico falls out of the bouncy castle, and is too tired to move and gives a couple of exhausted groans before the castle deflates and he falls asleep. The sweetest part is when Skipper picks him up and carries him over his shoulder back to their own HQ.
- A moment that's shown in "All King, No Kingdom" and backed up by "The Lost Treasure of the Golden Squirrel" is how much Maurice and Mort mean to Julien, even if he doesn't acknowledge it, to the point where Julien's deepest desire in "The Golden Squirrel" is shown to be his kingdom with Maurice and Mort in it.
- Even if it is rather obsessive at time, Kowalski's (ultimately one-sided) crush on Doris the Dolphin is very sweet.
- In 'Tangled in the Web' when Alice grabs Private to take him away, Skipper leaps after her to save Private, who cries out for him. Skipper in turn cries out, He's just a boy!
- In 'When the Chips are Down,' Private and Mort get stuck in a vending machine, leaving the others to worry what happened. After some failed leads, the team is reunited and Skipper is so happy that he's hugging and crying over Private, who's confused but happy.
- Kowalski's absolutely Adorkable fanboying over Invexpo at the beginning of "I Know Why That Caged Bird Goes Insane" is mixture of this and funny. And so is his fanboying over sneaking into laboratory full of various weapons in "Thumb Drive". Really, Kowalski's fanboying over ANYTHING is Adorkable.
- The fact that the Penguins always go along with Kowalski's inventions and are genuinely happy for him when they work is very sweet. And that despite them almost always ending up backfiring.
- Relationships between the titular penguins in general. Sure, they mostly treat each others as coworkers and they get into arguments very often, but there are times that show just how much they care for each others. For example:
- Skipper constantly treats Private as an adorable little kid and sometimes even acts like a caring (if misguided) father. In fact, Private has the role of the "innocent" of the group in general and they care about him for that very reason.
- Private looks up to Kowalski, is the only one who doesn't mock him for his love for science and Kowalski acts like an older brother to Private in return.
- Because Rico is the way he is, Skipper, Kowalski and Private really care about him, accept his quirks but are there if he somehow endangers himself or those around him.
- Roy and Bing helping the penguins sneak out to the Lunacorns On Ice performance.
- Skipper and Kowalski installing the Lunacorn chip into Rico's Miss Perky doll in "Hello, Dollface!" Rico is absolutely over the moon- no pun intended.
- Later, when Rico thinks that his Miss Perky doll has broken up with him, he hugs Skipper. And then Kowalski re-unites Rico with his doll by pretending to be her and saying "I like Rico just the way he is."
Heartwarming / The Penguins of Madagascar