Sakuya's reaction when she sees Tenchi after she got Stood Up by him, and she sheds tears despite trying not to:
Sakuya: Masaki-kun, you're an horrible liar.
Sakuya's Heroic BSOD when she realizes that she's got no real memories of her own;
Sakuya (in a Troubled Fetal Position on the floor of her apartment): T-Tenchi-kun... help me... please...
Yugi's backstory, specially as she's imprisioned inside a dark tomb after almost destroying Jurai, crying and screaming because she's scared of the dark. Made worse when Empress Hinase, the one sealing her away, is shown crying too, since she hates the idea of doing this to Yugi but can't do anything else