Also in Cross Days What does Yuki do when he meets Makoto for the first time? He punches him in the face and calls him out for cheating on Kotonoha with his harem.
Another one in Cross Days and only applies to Yuki's true route. Makoto finds out that Taisuke has been gang banging and blackmailing Yuki who is "Yu" at the moment. He stands up to the rapists and is called out for playing with girl's hearts. Makoto announces that he only loves Yu and won't let anyone hurt her even if it's his best friend. He gets beaten up as a result but Makoto breaks his friendship with Taisuke and stays with Yuki.
And another Cross Days one in Yuki's true route when Makoto was willing to run across the train tracks to get to Yuki. However, he wouldn't make it so Yuki jumps in and saves them both from being killed. This game just generates these moments when concerning Yuki.
In the Cross Days manga, Yuki is about to throw himself in the path of a train after not only he finds out Makoto is with both Kotonoha and Sekai, but Kotonoha harshly calls him out on the Yu thing. And then Roka goes Plucky Girl and pulls a Diving Save, tackling him away and saving his life, and later they stay together. Again, Yuki either is a CMOA machine or he inspires others to be awesome.
Kotonoha's Big Sister Instinct moment in Summer Days. When she finds out that Makoto had been putting the moves on her (underaged) sister, she clobbers him over the head with her father's golf club. And this is Kotonoha we're talking about.
Makoto in the entirety of the "All Hers" route. To clarify, Taisuke and Kotonoha are dating, but she breaks up with Taisuke because she still loves Makoto, and can't give up on those feelings. She and Makoto start to get along again. But Taisuke shows up the next day bummed about Kotonoha breaking up with him, which causes Nanami and Hikari to spread nasty rumors about Kotonoha get the girls from the sport clubs to bully and threathen her to stay away from Makoto so Sekai can be with him. They also help Otome and her posse bully Kotonoha, tipping them about the lunchbox she made for him, which prompts them to knock it down and step over it, causing Kotonoha to break in tears. When Makoto hears about all that, we see him enter the mother of all Tranquil Furies, call Nanami and Sekai out on their actions and warn them that if they keep this up, he will get angry, which makes Nanami realizehow much she just screwed up thingsfor the very one person she wanted to help, then stopping Kumi from slapping Kotonoha before calling Otome out on her treatment of Kotonoha, outright putting a stop to all the bullying Kotonoha's been suffering. There's a reason why this is regarded as Kotonoha's happiest ending.
Conversely, the finale of the "I Love You" route. In this route, Makoto dumps Kotonoha for Sekai very early on, and Kotonoha reacts extremely badly. She decides the best way to win him back is with sex, and starts seducing him so aggressively that it'd qualify as sexual assault if not rape. The VN does a very good job of making the player feel just as helpless as Makoto in this situation; there's no way to avoid multiple sex scenes with Kotonoha once this route's been triggered, leaving you to watch impotently as Kotonoha totally ruins Makoto's relationship with Sekai. After enduring through two whole episodes of this, however, Makoto finally manages to stand up to Kotonoha, shoving her across the room when she tries to rape him in his own bedroom, and the next day at school Makoto and Otome give her a brutal Reason You Suck Speech which finally, finally makes her back down. Yes,Otome. It's extremely cathartic to watch Kotonoha break down as the pair call her out on her craziness. Then Makoto manages to make up with Sekai (with Otome's blessing), but that's a different trope.
In Shiny Days Kotonoha kills Makoto and Nanami's boyfriend Kyouichi for forcing sex on her sister Kokoro. And with a katana! And then she sets the building they are in on fire and gets both herself and Kokoro out. Bonus points for being the first time that Kotonoha put an end to Makoto.