The special present given by Hibiki to Kosukegawa for his birthday, which is a scarf that Motoko and all of the HiFuMi knitted for him, as well as Kosukegawa comforting Mikiri after her fight with the guys who ruined "Granny"'s odango. Also, see Right Behind Me below.
The ending scene that transitions from Kosukegawa crying after realizing HiFuMi and Motoko are one and the same now, to him crying as he and his daughters take pictures with the Kamen Raiders.
HiFuMi figuring out their true parentage.
Fujiko: You're right...it really is a miracle.
The reconciliation between Ginga and Gadam (i.e. Izuru Hino).
Kosukegawa's first encounter with Zero, starting from here, is a mixture of Tear Jerker and this.
The image of HiFuMi and Motoko all working together to stop Zero from killing Kosukegawa. Sure, it's just a metaphor, but damned if it isn't a powerful one.