Ennis breaking down in tears after meeting Isaac and Miria for the first time. The novels drive it home by stating that this was the first time she had ever genuinely smiled or cried.
A couple different times with Czes; when he's rescued by the magnificent duo and they tell him he's a good boy, and when he is reunited with Maiza.
The ending theme. It will bring tears to your eyes, no matter how lighthearted the series is.
Nice accidentally blowing herself up. Becomes even more heartbreaking when you realize that she was "eight" at the time.
It gets especially tear jerky when Jacuzzi shows up with a gaudy tattoo on his face so his face will stand out like Nice's (which is now permanently scarred) and she won't feel so alone. And then they both cry; Nice because she's so moved, and Jacuzzi because that's just what he does.
The end of Bullet Garden when Illness breaks down after hearing a hymn of SAMPLE over the phone