The ending of the anime is particularly notorious—even having one of the scenes in an AMV can bring people (or at least this troper) to tears.
"I'm just... so scared, Chrono. I don't want to die!"
The ending of the manga also brings out the tears, starting with these words: "Rosette's life...came to an end in March of this year."
Not to mention the near volume-long flashback that reveals Chrono's long avoided backstory. Particularly the completely silent section—no dialogue, no sound affects, no narration—showing Mary Magdalene's death at Chrono's hands. It's a shame the anime rushed through it.
This manga full of it. When Chrono realized what he had done during his rampage in San Francisco, when Rosette awakens Chrono from his self-induced coma, when Satella freezes herself together with her older sister, when Joshua rips out his horns realizing that he don't need it to become strong, Rosette's near death experience, and the effect it has on Joshua and Chrono, and in the epilogue where Satella watching Azmaria's tape.
What about the scene when Mary Magdalene gives her life to save a mortally wounded Chrono? This troperette cries even when she only thinks about it.
Both the anime and the manga have an ending that causes the tears to flow. Chrono's backstory is another tear-jerking moment.