Ninja'd by the other girls/women
But the ending-ish of the first story arc of Naruto
[spoiler/] Sasuke sacrifices himself to save Naruto, and "dies" in his arms; Naruto gets talked into killing Haku (I know neither of those actually end up happening, since Sasuke lives and all that, but it still gets me); Sakura breaks down over Sasuke because a)she loves him and thinks he's dead; b)she feels like she isn't allowed to cry because of the ninja rules; and c)they're all TWELVE; Zabuza has an awesome yet incredibly depressing fight with/getting stabbed by a bunch of thugs; Kakashi and Zabuza's manly/...ninja-ly respect for one another, particularly when Kakashi carries Zabuza over to Haku's body; and Zabuza's whole death scene.
Sorry about the venting, but this more than anything else made me appreciate that for all the silly moments in Naruto, the writers do recognize that this is a pretty dark world for kids to be running around in, and they hammer it home in the team's first real mission. [/spoiler]
did get the tears flowing.
Also, the novel "The Book Thief." I knew it would be depressing going into it because, well, it's WWII Germany. I don't cry very easily, despite the above, but I had a flood of tears going for the last hundred pages. Not very manly, in retrospect, but I challenge you to read it and not cry.