Tear Jerker / Gunslinger Girl

• Numerous portions of Gunslinger Girl, especially the backstories of the titular assassins, make almost any reader cry, cringe, or both. Triela's past in Snuff Film in particular raises the question of how much of a blessing the Conditioning is in a lot of these cases. Of course the mental disintegration of the kids is not easy to watch either — and neither is Angelica's eventual death after she protected her handler from a bomb attack. They really drive the point home by letting her tell that Fairy Tale to cheer up her handler, right before she dies. Doubly so as she doesn't even remember who he is, telling him the story that he told her.
• The whole blasted thing. Special mention goes to the Claes-focused episode in the first season.
• And then there are the events in chapters 83 and 84. Holy schlamoly.
• Triela's eventual discovery of how she and her handler came to the "Social Welfare Department", and how they choose to face her approaching mortality.
• Everything about the deaths of Enrica, Sophia and Giuse and Jean's parents. Made much worse by how it happens just as Enrica had accepted Sophia as her sister in law. She even dies as she's about to make amends.
• This scene from "A Day in the Life of Claes"
  Claes: Have you ever been tremendously sad, but the tears won't come out?
  Jean: Sure...it happens.
  Claes: That's how I feel right now. My heart is overflowing with tears, but they just won't come out of my eyes. At night when I'm asleep, they quietly spill out onto the pillow without my noticing.
• Henrietta fulfilling her earlier suicide pact with Giuse at his request. After getting fragged at her hands during a rampage, he has her finish the job and, as she does so, puts a bullet through her head. This was made more poignant by the fact that 1; Giuseppe, had enough with his guilt, had loudly declare that he won't let his guilt define who he is, that could mean his relationship with Henrietta could improve again in the future. 2; Henrietta had fragged him by mistake, not because of any ill intent or revenge toward Giuseppe, but because she can't discern him from the enemies during her trauma-induced berserk moment. Wait, now I get it. If Giuseppe really paying attention toward Henrietta's mental condition, he should know that Henrietta had trauma concerning people with balaclava.... Oh well, too late to do anything about it now.
• The anime intro, using the Delgado's "Light Before We Land", is a painful, heart-wrenching summation of this entire series: yes, these children are trained killers, but they're still children. The first time you see the intro, don't be surprised if you miss the first few minutes of the episode following as you try to stop crying.
• Henrietta being reconditioned is horrific. She's always been a happy, friendly kid and she's the protagonist. Suddenly all her memories are gone and her personality is reset to a complete blank.
• How the battle with Giacomo Dante ends. He grabs Jean and attempts to use him as a Human Shield, but Rico, having earlier been instructed on this exact situation, shoots through him anyway. Afterwards, Jean thanks her and tells her to move on and accept his death, and she starts crying and begging him not to leave her alone, saying that he's her only reason for living. For a pair that has had very few emotional moments together during the series, it comes right out of nowhere.
• Petra didn't die in the line of duty. She died from something as natural and inescapable as cancer. Even with all the advanced technology they couldn't cure her. Or rather, they could have but the cost of doing so and extending her life until she'd die anyway due to her cyborgization was deemed too high. Not that that makes it any better.