Seeing Nico actually tear up when she learns about Guy and Beldo, and worries about your safety in the monster tower.
Also seeing Cherrl outside and able to walk after being sick for so long just because your friendship motivates her so much, and then standing up to Ghosh when he insults Koh, and passing out due to the stress and exhaustion just to help Koh out.
And there was also the part where Mia comes out of her shell and realizes how beautiful she truly is.
The best ending also qualifies for this. It's a shame you can only see it once per save file.
When you forgive Kewne for betraying you at first when you discover he's a pawn of Beldo at the end. There's a happy sprite afterwards showing just how happy he is, and it shows him nuzzling against you after he happily yells Koh's name.
In Nico's storyline, there's the moment where she finally realizes the kind of person Ghosh is, and seeks redemption from you. She tells you it's fine to hit her, but one of the text options makes Koh talk about some of the final words his father ever spoke to him, where Guy told Koh to take good care of women. Nico's reaction where she's pleasantly surprised and bashful with what you say makes the moment even better, the moment being the one where she finally realizes her feelings for you. In addition, it's showing that Koh took to heart the words of his father and still acknowledges him as a role model.
Koh and Ghosh actually agreeing with eachother and teaming up to help Vivian feel better. Ghosh even lampshades this.
The moment Cherrl confesses to Koh, especially just on how much he's helped her.
Cherrl: Give me a chance to express my appreciation. Thank you. Not only for bringing the Healing Herb for me, but for everything, ever since we first met. I'm glad it was you, Koh, that brought Chuppy to me. Giggle... so there you have it. Huh... That's a load off my chest. I just wanted to tell you how I felt. It's the first time ever that I've used up so much courage...thanks to you for that too, Mamoru. Thank you.
Another is her long, final speech. About how she wants to marry a certain someone (obviously Koh). Despite the English translation team screwing up a Title Drop (sky-colored dream), it is very heart-warming.
Cherrl: Hey, Koh. Sometimes I think of the irony. Until not too long ago, I would spend every day looking out the window and gazing at the blue sky. Right now, I'm in that dream outside of that window. Yes, life can be so unpredictable. If I wasn't so weak, I might have been able to have many other wonderful days in the past. But on the other hand, I might not have met you, Koh. Even when I was ill, if I hadn't thrown that stuffed doll out the window, I might never have met you. Every time you meet someone, every time you make a choice, life itself changes, right? I had hated my life so much in the past, but now I've realized that my life is the same color as this sky. The color of the sky has always been the color I adored the most. It's the color that symbolizes the world outside the window, and also... My sky colored dream... is to be married to a certain sombody. But if I do marry that person, he's likely going to make me worry, which might make me sick again. Even so, I'd probably be the happiest woman around.