The climax of the Ryuuzetsuran route, culminating in Hideo and Cap managing to talk Jun out of blindly following Touma, and the two of them recanting their ways. Their reunion with Koyuki is also quite touching, especially given the ending credits that played just beforehand - Koyuki in a Troubled Fetal Position, surrounded by photos of the trio together, as "Winter Fireworks" plays slowly in the background.
Momoyo carrying Yamato piggyback at the end of episode 5.
Kyouki's route in S, especially if you've played the original. It's a Tear Jerker in the good way.
In the Cookie 4 IS route, IS is about to have her memory wiped after the other IS models rampaged around. She accepts it since the alternative is forcing Yamato, her chosen master, as well as the Kazama family to make enemies out of Kuki. They instead decide to break into the Kuki laboratories and save IS, but are caught by the servant unit led by Mikado, the Kuki head, himself. Yamato resolves the situation by taking the blame by pretending to have threatened his friends and agrees to work for Kuki and pay of an incredibly large debt caused by their disruption. Yamato tells IS that she's more than worth it. Unsurprisingly, both Cookie and IS kiss Yamato for it, and in front of the family no less.
Almost the whole of Monshiro's route. She and Yamato are together pretty much constantly throughout since Yamato becomes her personal servant while helping her do some talent scouting for Kuki Corp, though surprisngly, she and Yamato don't actually become a couple until very near the end of the route. There's just so many "Awwwww!" moments, but the biggest one has to be after their day out at the aquarium where Mon kisses Yamato on the cheek and says it's to show he's her favorite. The bashful smile she has on her face as she says this is just precious.
Yamato's relationship with Kokoro in Azumi's route in A1. They weren't fond of each other at all back when Yamato was in Class F (since Kokoro made a habit of insulting Class F whenever she could) but once Yamato moves up to Class S in Monshiro's route, Kokoro pretty much instantly accepts him into the class and lets him know he can ask her if he has any problems. In A1 the player has the option of talking to Kokoro at certain points, and though she acts like it's no big deal, she does clearly appreciate the fact that Yamato keeps her company.