* Kikaijima and her senpai value money more than their lives, but they also value each other more than money.
* After getting up from being turned into a human pincushion in his fight against Munakata Kei, Zenkichi is visibly pissed, not because of the five blades sticking out of his back, [[BerserkButton but because Munakata dared to make Medaka cry]].
* [[http://www.mangareader.net/215-46730-13/medaka-box/chapter-36.html GO GET HIM, TIGER!]]
* Definitely understated, but Munakata's backstory. [[spoiler: Munakata's killing impulse is the real deal, so he had himself branded as a wanted criminal and purposefully isolated himself from others in order to avoid killing anyone. His main reason for joining the Flask Plan was to find people strong enough that they could survive being friends with him.]]
** And of course, Zenkichi is badass enough to do just that.
** Zenkichi manages to do something similar in later chapters, being able to convince Emukae Mukae that just because she was a Minus doesn't mean she couldn't be accepted.
** And of course we can't forget how Zenkichi pretty much persuaded Medaka that it was her purpose in life to make the people around her happy.
* Zenkichi accepting Shiranui and declaring her his friend, even though she'd just made herself his enemy and seemed to be trying her hardest to alienate him.
** [[http://www.mangafox.com/manga/medaka_box/v08/c066/14.html "There's no way I can stomach something so sweet."]]
* Kujira realizing that why she [[spoiler: couldn't betray Medaka and company]].
--> '''Kujira''': "I like them too much. [[spoiler: So while I can betray my friends]], I can't betray myself."
* Zenkichi's [[spoiler: HeroicSacrifice]] in the Manager of General Affairs battle against Kumagawa.
* Hinokage finally getting the recognition he deserved while fighting in the Vice President battle -- that translates to an entire school cheering for the Unknown Hero.
** What makes the above entry all the more heartwarming is that Hinokage had been helping everyone despite the fact that almost no one could remember whom he was because of his ability.
--> '''Hinokage''': "I held pride in protecting everyone without anyone noticing or realizing it... [[ManlyTears but it really is great -- being cheered on by everyone, being appreciated by everyone]]."
* Medaka's fight with Kumagawa ultimately culminates in one that overlaps with an AwesomeMoment:
--> '''Medaka''': "Crawl back up, Kumagawa. I look forward to the day that I get to save you!"
** In the same chapter Kumagawa apologizes to Class Minus 13 for losing, and declares that it wouldn't matter since he would willingly sacrifice himself to protect the Minuses.
** And then we have Class Minus 13 saying Kumagawa was already doing that, that it was now their turn to protect ''him'', and promising to improve their ways once they saw that even someone like Kumagawa could be reformed.
*** It's also a heartwarming moment for Kumagawa; his defeat by Medaka is the first time that he's lost properly. Not because of fate, not because of his Minus, but because of only himself. It was the kind of defeat that helped people get stronger afterwards, giving him the hope that someday, he'll win.
** We also have Medaka telling Kumagawa that she needed him in the Student Council.
* Takarabe refusing to apologize to Aka, because Aka bullied her friends. Despite being scared to death.
** Kumagawa winning against Aka just to get her to apologize to Takarabe and her friends for looking down on them because they didn't have an ability (and maybe get the nurse to go NakedApron).
* In chapter 119, Kumagawa announces that he's willing to support Kikaijima in stopping Anshin'in's plans.
* Munakata willing to break his [[ThouShallNotKill code]] in order to help his friends, despite being somewhat aware that his intentions won't justify his actions.
** Of course, Kumagawa protecting Kikaijima from Munakata, commenting that he feels happy dying for a girl's sake.
** And Medaka's successors opting to follow Kumagawa, saying that [[spoiler: in order to return things to normal]] they're willing to make as many enemies as needed, including Anshin'in herself.
* In a meta-example, there's something inexplicably heartwarming about Kumagawa's total and complete victory in the second character poll. Seeing him cry tears of happiness at finally winning for once (and, one assumes, for [[HadakaApron other things]]) is rather touching.
** What truly makes it heartwarming is that this is a character who has never fairly won anything in his life. Ever. And has never had anyone really like him for who he is who wasn't a minus. Ever. And he won a popularity contest. Against the main characters of the series. And he didn't just win, he dominated to the point that he got more votes than the 2nd, 3rd, and 4th runners up. COMBINED. When Kumagawa declared his true intentions, he ended it with saying "I want to prove that I'm better than the main characters!" You are, Kumagawa. You are.
* Akune coming to terms with his feelings for Medaka, allowing himself to finally be able to move on and go all out.
* Though there is an undercurrent of manipulation from Ajimu, it's definitely heartwarming to see how many people are willing to support Zenkichi in Chapter 122. Maguro, Naze, Shiranui, Emukae, Munakata, and eventually [[spoiler: Akune]].
* In chapter 126, Emukae [[IWantMyBelovedToBeHappy sets aside her own feelings]] and declares that Zenkichi's "selfish" love for Medaka isn't wrong, because it's love.
* Chapter 128: Ajimu asks why Shiranui is [[IWantMyBelovedToBeHappy helping Zenkichi get with another girl]]. Her response?
--> '''Shiranui''': You see, unlike justice, love does not always have to win.
* Medaka mentioning that she's proud to have once earned Akune's affections.
* Chapter 139: [[spoiler:Zenkichi telling Medaka that she has to find her own reason for living, then telling her that her speech about "living for strangers" is wrong, and that no one at the school thinks of her as a stranger anymore.]]
* Chapter 168: Najimi and Kumagawa's final conversation, when she hugs him and tells him he is strong and that she loves him.
** In the same chapter, when she blew up a star for him.
* Chapter 176: [[spoiler: Zenkichi forgives Shiranui for her JerkassFacade after all the trouble they've gone through.]]
* Chapter 184: [[spoiler:Iihiko's "echo"]] comforting Medaka as she tries to psych herself up for a course of action that may likely result in her death. For just a moment, we can see why this guy was considered a hero.
* [[spoiler:When Medaka finally returns. Kumagawa can be seen crying. He truly missed her]]
** [[spoiler: Just as heartwarming is the words they exchanged when she returns. He bet her that Medaka would return in time for the graduation ceremony and Medaka admitted she lost. Kuamagawa tears up when he declares "At last, I won!".]]
* Chapter 190: [[spoiler:Kumagawa reveals that on the back of each flower of the bouquet's nameplate is a message from its owner. It's overwhelming seeing how much people are going to miss Medaka.]]
* Actually, the ''whole'' finale of the manga is being one huge CrowningMomentOfHeartwarming, with [[spoiler: the battle with all the characters of the manga in a run, bar Anshin'in]], the end of chapter 190, and [[spoiler: the WhereAreTheyNow moment in the final two chapters]]. A satisfying ending to a manga that was certainly different from Shonen Jump standards.
* In chapter 192, a 'ten years later' chapter, Zenkichi challenges Medaka to a final duel to settle things. If he wins, she marries him. She accepts, conditioning that, if she wins, he has to marry her, promising that they won't ever say goodbye ever again.
* [[spoiler: All the students Hinokage helped out while he was President finally remembered him and came to cheer for him at the Vice President Battle]]
* The final image of the series, straight at the final chapter. It includes a picture that marks the end of high school for the main cast. The participants include [[http://a.mpcdn.net/manga/p/681/425823/23.jpg Medaka, Zenkichi, Shiranui, Kikaijima, Akune, Misogi, and Najimi]]. The kicker: The messages left by Najimi - "Let's play again sometime." [[FireForgedFriends Shows how far they've grown as people and as a group]].