In the Otome ending, where Makoto pours out his feelings to his little sister, and explains his idiocies in a way which makes sense to a young child, and Itaru's commentary, which is quite sweet.
Late in the anime, Makoto sees Kotonoha in the park and apologizes to her. The Christmas carols make it so much sweeter. And then it's cruelly subverted in the end.
In the anime, when Kotonoha first stands up to Otome and her crew by telling Otome that she is Makoto's girlfriend, and that Otome attacking her won't change that fact.
The "Only You" ending of Cross Days. When his true identity is revealed, Yuuki tries to run away but Makoto won't let him. Yuuki asks him why he's so persistent even though he now knows that "Yuu" is really a boy. Makoto replies, "I know. But I still like you," after which Yuuki finally gives in to his feelings for Makoto and cries. Cut to the two of them in bed, holding hands, making some small talk before Yuuki worries about what they should tell Kotonoha, to which Makoto tells him not to worry. The next scene is the cherry on top, with Makoto whispering to Yuuki, "You are my number one boy". Almost makes up for all Makoto's dickishness in School Days.
The Christmas Eve ending of School Days is a CMoH for Kotonoha, and Tearjerker for Sekai. Most endings where Makoto commits himself to one girl, and reject his indecisive ways, are this to some extent.
The "Elder Sister" ending of Cross Days. After Kotonoha overhears Makoto having sex with Yuu(ki) and has completely lost it, she goes to the library to kill "Yuu". At the same time, Chie (Yuuki's older sister) is looking for him and discovers that Yuuki and "Yuu" are the same person, because of his female clothing that he stored in the library. Kotonoha, who overhears Chie calling for Yuuki, accuses her of being Yuu. To protect Yuuki, Chietaunts her and dies to protect her brother. Even though Chie was a jerk to her brother, she still loved him enough to save him from someone who is murderously gone.
Makoto saving Kotonoha from her bullies, and outright putting a stop to her bullying in the "All Hers" route. Complete with the following line:
Makoto: This is my business. I'm her boyfriend. That's why I can't just stand by and watch her get hit.
What, no love for Sekai? How about the Bavarois Ending where Sekai's mother encourages her to reconcile with Makoto, or how about her own Christmas Eve ending where he chooses her?
Sekai: *Hugs Makoto* I've got the best present ever.
No love for Two Lovers either? Yeah, pregnancy, but Happy Ending.
From the same chapter, Roka comforting Yuuki when he's having a Heroic BSoD after Kotonoha tells him not to come near her again after she finds out he was crossdressing as Yu.
Yuuki: Don't act like you understand! I've lost everything, don't you see!?//
Roka: I'm still here!! The person you saved! Me! Am I not good enough proof of your persistence!? I'm still standing here! Isn't that enough!? Get a hold of yourself! You're a man, aren't you!? So don't...say something like "It was futile"...! If you don't think it had meaning, then no matter how long it takes, I'll wait for you until you do!
Reaching Setsuna's Golden EndingWith My Family. This requires Makoto to not give Sekai false hope and stop blaming Setsuna. Once it becomes clear to Sekai that Makoto's heart will never belong to her, she arranges for Makoto to reconcile with Setsuna. Oh, and this particular ending has Shun successfully overcome his womanizing habit and reconciles with Mai as well.