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 is 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.
In the true ending of Cross Days, Yuuki realizes that he loves Makoto but thinks Makoto is only interested in his female persona Yuu. He intends to break up with Makoto before he finds out his identity after Makoto saves him from Taisuke. Makoto won't take "no" for an answer and continues to be persistent. Naturally, Yuuki tries to get off at a different stop so Makoto won't follow him, but Makoto forces his way off the train shortly after. Makoto finally declares his undying love for "Yuu," which upsets Yuuki greatly. Makoto intends to rush over to the other side of the train stop despite a train coming. Unlike many of the bad endings where everyone watches someone get run over, Yuuki jumps in and saves them both from getting hit. His wig falls off, revealing his gender. Yuuki tries to run away but Makoto won't let him. Yuuki finally asks him why he's so persistent. Makoto replies, "Yuu and Yuuki are the same person. If I said I love you, I love you." Naturally, Yuuki finally gives into his feelings and cries into his shoulder and Makoto is redeemed for all the assholism he does 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.
Even in the bad ending of Cross Days there's one: After Kotonoha overhears Makoto having sex with Yuu/Yuuki and has completely lost it, she goes to the library to kill him. At the same time, Chie (his 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 overheard 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 saved 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 persistance!? 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 require Makoto to not giving Sekai's 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 overcomes his womanizing habit and reconciles with Mai as well.