This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Cyber Team in Akihabara
Hibari's affection for Densuke, especially when you learn why she named him Densuke. It's in memory of her stillborn baby brother.
Episode 18 has Takashi's lack of respect from his father despite everything he's done, leading him to arrive at Jun's apartment in tears.
Episode 19 has the Sibyl Team's passionate declaration of love towards Takashi, even if it means they're martyrs for it, which even stuns Hibari.
Also, Takashi attempts to turn himself against Chistian by attacking the Cyber Team girls by himself, but cannot bring himself to deal the final the final blow to Hibari because he was conditioned by Christian into loyalty. As he realizes this, he has a breakdown and cries as he lies in his collapsed armor.
Also, Tsubame sheds a Single Tear for Takashi, after realizing both are clones of Crane, but while Takashi choose to be loyal to Washuu, it backfired on him horribly.
Episode 20. After witnessing Takashi's breakdown and abandoning the town, Tsubame walks around Akihabara confused about what to do with her life until Hibari invites her to her house. Tsubume suffers an emotional breakdown when she sees how a loving family behaves.Hilary Haag captures it perfectly.
Tsubame Ohtorii: "You're nosey, Hibari... It's not fair! Why should you have everything? Why is it always about you? Hibari has a father who loves her! Hibari has a mother who loves her! Everyone is doting all over her! Hibari has a place to go home to! Why do I have nowhere to go? No one doting over me? It's just not fair! All I want is..! ...Is..." * sobbing*
Episode 25, when the girls are spending their last day on Earth before leaving, and are contemplating all the loved ones they'll have to leave behind.
Episode 26, when the Pata-pis all develop souls and free wills and decide to go with Crane in the girls' place, and all the girls, even Tsubame, are crying and begging them to come back.
The Stinger was a bit depressing when it shows Takashi in a train with a younger clone of Tsubame and attempts to forge a relationship similar to the one Crane had with Hibari. Yes, he's still attempting to please his father and "be Crane"