The ending of the last episode of Kino's Journey got me.
Considering that you see her meet all these lovely characters, decides that she won't stay longer than three days (even though she wants to), leaves the third day only to bear witness to the entire city being buried under lava. I cried like a baby.
The scene in Fullmetal Alchemist from the 7th episode,
when Ed finds the remains of the chimera created from Nina. It's a certified tear-jerker.
And there were two scenes from Monster that made me want to scream bloody murder.
1. When Johan (as Anna) convinces Milosh to go to the Red Light District to look for his mother.
In the process driving the kid to nearly jump off a bridge. Johan's words, if I remember, were: "Were you born because you were wanted? Why were you thrown away?". Mind-fucking a kid = really damn cruel in my books
2. Most of Episode 29 made me want to hurl a brick at Johan for being an immense prick.
Well, when Johan and Robert cross paths is the main part where I got emotional. The whole talk on the rooftop which resulted in driving Robert to drink again (and it's debatable as to if Robert's death was suicide or if Johan pushed him) made me so mad...I mean, Robert was just trying to turn his life around. Arsehole.