Chapter 14. Asuna having Negi spend the day with Ayaka on what would have been her stillborn little brother's 10th birthday.note Given Ayaka's monologue, she only brought that up once then tried to forget about it, so Asuna remembered that after ten years. Negi ends the day by writing "Asuna-san's close friend" next to Ayaka's picture in the class roster.
Chachamaru feeding kittens. And saving kittens stranded in water. And this was back when she was just Eva's emotionless assistant.
In fact, if you read some of the things that the children following her are saying, you learn that the good deeds she's doing (getting a kite that was flying away back to it's owner, a little girl; helping an old woman up a flight of stairs by carrying her on her back, and saving the kitten) are actually typical actions of her, and that nothing is odd about her doing it.
In chapter 118, when Negi meets with his father for whom he was looking for his whole life. Doubles as a Tear Jerker, since it's just a duplicate which will disappear in ten minutes. Nevertheless, it is the happiest moment in Negi's life.
The bit afterwards with Evangeline in one of her rare "cute" moments just adds to the effect.
Chapter 128: Yue has just confessed to Nodoka that she's in love with Negi. She then starts screaming that she's a terrible friend and it would be best if she just disappeared, which results in Nodoka slapping her. Now fully convinced that her best friend hates her, Yue seems like she's going to just run away, and most likely kill herself. But then this happens.
There are a number of these connected with this love triangle:
The Saishoudoukin incident, while rightly on the Crowning Moment of Funny page, arguably qualifies as this, as it signifies that Nodoka will not sacrifice her friendship with Yue for anything. Not to mention the fact that in the second image, it's Yue who's on top of Negi while Nodoka looks on.
During the holiday at the beach just before the trip to Wales, Nodoka and Yue have a somewhat heated argument where each tries to convince the other to ask Negi out the next day. It doesn't take long before they start laughing over the fact that they're "rivals in love".
In Chapter 286, Yue and Nodoka's conversation about her amnesia. Yue mentions that she only remembers clearly her life up until the winter of their second year, and remembers nothing about Negi. Nodoka does not hesitate for a second before telling her that they were both in love with him. It's subtle, but it still represents Nodoka not using the situation to her advantage.
Then there's chapter 214 when Negi and Asuna meet after long period of separation in the magical world. Justtoocute. The fact that she always tried to maintain a tough front and not show how much she cares about Negi makes this outburst of her real feelings that much more heartwarming.
And in chapter 77 where Asuna is heartbroken after she saw Takamichi and Shizune on what appeared to be a date (It wasn't) and runs off followed by Negi. When he catches up to her she is already in self-loathing mode and starts to criticize herself claiming that she isnt someone to be liked ... only to be stopped by Negi who lists her virtues and says the ''he'' likes her.
Asuna: I am so stupid and violent that I've got only a few friends... Plus my personality isn't the one loved by others... Even Takahata...
Negi:THAT... THAT ISN'T TRUE! Asuna is always so... steady, determined and beautiful... I... I've always liked you too...
Another Negi/Asuna CMOH happened in issue 62. After stewing at him for the past three or four issues, Asuna goes out in the middle of the night to talk to Negi. After playfully jerking him around a bit, she strides toward him with a serious expression, looking like she's about to hit him. Instead, she catches him in a tight hug, apologizes, and tells him just how much she cares about him. Finally, she asks him to consider her his official partner, solidifying their Battle Couple status.
In Chapter 209, cynical Meta Girl Chisame is watching over Negi's unconscious body as he undergoes his trial for Dark Magic. She's been warned that if he doesn't wake up before sunrise on the second day, he may never wake up again. Sunrise is fast approaching and Chisame is getting very nervous. She starts talking to Negi, telling him that he seems to have a lot of faith in her and how that's kind of a big deal for her, as she's always been the onlooker. She grabs his hand and tells him that she believes in him...but then she starts wondering what she will do if he never wakes up, what she will tell her classmates. She grabs the knife that will break the trial scroll, apologizes to Negi for not believing in him to the end, and stabs down...only to see Negi catch it with two fingers, sit up, and tell her, "Good morning, Chisame-san. I'm all right now." She starts to tear up, Negi asks if she's all right...and she starts beating on him with a pillow, yelling at him for waiting till the last second and accusing him of putting her through hell. Jack Rackan shows up and tells Negi that Chisame stayed up nursing him for two days and two nights straight.
One of the earliest CMOH is in chapter 50, when Setsuna reveals her wings, being part demon. After that, she decides she should leave, since Konoka will probably hate her, until Asuna smacks her in the face.
Asuna: What are you talking about, Setsuna? Konoka's your childhood friend, and you've been watching over her from the shadows for two years now. What have you seen during that time? Do you think Konoka is the kind of person that would hate you just for something like this? You're such an idiot!
And then there's Konoka's reaction upon seeing Setsuna's wings.
Chapter 252 had a real heartwarming moment between Konoka and Setsuna. Setsuna spends a good chunk of the chapter angsting about how she's unworthy of protecting Konoka, and is essentially torn between her ability to protect Konoka, and her desire to be friends with her, believing that her happiness is making her weaker. Turns out Konoka was aware of Setsuna's cycle of depression, and promptly gives her the best encouragement possible:
Konoka: Being happy isn't something that makes you weaker. Happiness can make you stronger than ever before, and helping out those people who aren't happy right now, or who are going through all different kinds of trouble... That's the job of a Magister Magi. [...] I'm going to become a Magister Magi someday. A great mage like Negi-kun's father and mother, and I was thinking it would be great if when I do achieve that, Secchan... You could be by my side as my partner, like you've always been.
Chapter 257. While the good-byes that the girls bid to their friends are very sweet, the conversation between Tohsaka and Negi where the first tells the latter what he thinks of his Missing Mom Arika is the most heartwarming moment in the chapter.
Chapter 262 Kotaro telling Natsumi that he thinks of her as a family was incredibly heartwarming, especially because she's the only person that he's expressed such extreme fondness for. She's also the only person that he's bonded with over something other than fighting, and he's the person least likely to express his feelings to anyone.
Kotaro: I sure do like you. Heck, I love ya. To be honest...I think you might be the most important person in the world to me right now...I've started to think of you as a real...a real family. You might be the only family I have in this world...saving the world...I think the one thing I think I gotta protect even if I die in the attempt is you, Natsumi-neechan.
And they take a page out of Konoka and Setsuna's book by getting into a pactio as well. Wheee!We hope.
Cute Ghost Girl Sayo's Day in the Limelight episode ("Verba volant, scripta manent") of the Negima!! (1st) anime. Although she's a Cheerful Child, Fridge Logic brings home just how heartrending her life must have been as an invisible, inaudible, and untouchable spirit; tied to one place and watching 65 years of classes pass her by. Then Kazumi gets up to ask Negi to add Sayo to the list. Aww. Then Evangeline frees Sayo from her isolation by making her visible and tangible. Awwww. Finally, the class gathers around in friendly welcome. D'awwww...
Chapter 74 of the manga qualifies for the same reasons.
Kazumi also gets a major heartwarming moment as up until this point, she's been portrayed as 2-A's version of a gossip journalist, but in this episode, she proves that even she has limits and refuses to take the photo of Sayo crying citing that it doesn't feel right.
There's also chapter 263, where Chachamaru suffers a huge bout of depression because she thinks that she doesn't have a soul because she's just a robot. Negi then proves her wrong the the most spectacular way possible. The pactio won't work without a soul, after all, and Negi is going to make it work—kissing her harder and harder—to the point of causing an explosion —until the laws of magic themselves cave in and give her a card.
Negi: I don't know who decides the laws of the pactio, but organization, spirits of the contract, or whatever you may be, don't you dare screw with me like this! This desperate, despairing Chachamaru-san I see before me cannot be a simulation! She cannot possibly be artificial! In fact, so what if she is artificial! Chachamaru-san is our friend!! She is real! And I won't let anyone tell me otherwise!!
Chapter 269. Nagi saves Arika from execution by horde of monsters in a valley where magic and spiritual energy don't work.
Nagi: You really aren't going to get it unless I spell it out for you, are you?! You damn sheltered princess! Why am I doing this?! Gawd, I'm doing it because I love you! Why the hell else?!!
Also, when Nagi badgers Arika to tell him how she feels, she, distraught, blurts out that "in the entirety of these two long years, not a day has passed in which I did not think of you! Well?! Is there something wrong with that?!" ...And Nagi simply smiles, warmly replies "No. Not a thing", and pulls her close and kisses her. If I wasn't a guy, I'd Squee! at this.
Chapter 297: Negi reunited with his parents. His perfect world was really just that... doubles as a tearjerker because it's pretty clear from the beginning that it isn't real...
Chapter 300 has this by a bucket, when Anya points out to Asuna that everything Negi does he does for her sake. Asuna then gets flashback in which Nagi express the same philosophy. Asuna then recalls how Negi was always trying to catch up to his father greatness even if this pushed him beyond his limits and decides that he already did. Cue Imagine Spot of Negi and Nagi coming to take her back. She then bursts into Tears of Joy
A bit of a villainous one in Chapter 301: Dynamis compliments Fate's minions on their successes, and thanks them for helping Cosmo Entelecheia.
It's small, but it shows just how much faith Konoka has in Setsuna.
309: Kotaro comforting Natsumi when she faints after having a close encounter with Fate. His understanding of just how much of an ordeal the mission is putting her through is really touching, especially as he's usually not the most emotionally tactful person.
Chapter 315: The lookon Chachamaru's face when she sees that Negi has come to save her and her friends. Negi gets one for telling Quartum that Chachamaru is not a doll and neither is anyone from the magical world.
Chapter 332 with the entire class (except Eva and Chao) joining hands to wake up Asuna, who is in a magic-induced coma of sorts. Not only it works, but when she wakes up, she thanks them all.
Chapter 334. Negi and Asuna's reencounter.
In Chapter 82, when Setsuna says that Negi is her savior (being a wingman for her inevitable relationship with Konoka, and gaining her a Heterosexual Life-Partner in Asuna), and that he's a special person to her. She then pledges to always come to his aid whenever need be, AWWWWWWW!!
Chapter 335: some of the reunion scenes after everyone who was erased were resurrected. Specially when Emily, Mama Bear and Kousaka return.
Chapter 337: When Negi allows Chachamaru to become his secretary. 
Chapter 340 somehow manages to be both a Crowning Moment of Heartwarmingand a Crowning Moment of Funny at the same time! On one hand, the sheer exuberance of Ayaka kissing Negi is so over the top you can't help but laugh - as Chamo points out, "His eyes are rolling back! He's twitching-!! what kind of Power of Love is this-?!" And yet, the fact that Ayaka's power of love was so great as to have that kind of effect is a very sweet recognition of a character normally relegated to the comedic.
This chapter also contains a beautiful Friendship Moment between Asuna and Ayaka: Ayaka thanks Asuna for keeping the promise she made before going to Magic World. Asuna thinks she is talking about keeping Negi safe, but Ayaka corrects her, saying that she knew from the start that Negi will be fine, and that she's happy that Asuna managed to return safe as well.
Chapter 344: Yue finally confesses her love to Negi.
Chapter 350: Asuna, Ayaka and the time capsule. Also doubles as a Tear Jerker.
Asuna: Negi and Nagi-San... Takahata-sensei... Konoka and Setsuna-san... I've met a lot of people since then. But, well... meeting you might have been the best luck I've had in my life.
The updated class roster in chapter 351 has a dozen crowning moments at least, but the the label on Setsuna's picture "Konoka-san's partner and mine." In so few words it says how deeply Negi values her.
And all of chapter 351, 7 pages of heartwarming, 6 Pages of bittersweet, 5 pages of tearjerker.
Chapter 352 is worse on all counts. Asuna digs up their Time Capsule and find not only the pictures of their school days, but also of the girls' lives afterwards (The Sports Girls stuck together even after college, the twins grew up (and pretty well, by Asuna's reaction), Satsuki became a master chef, Mana of all people was surrounded by children, Sayo was brought back to life), and final messages from both Negi and Ayaka.