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.