Fullmetal Alchemist:
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Hughes death, and every appearance of Hughes after I saw that, in credits, in past episodes, when he was mentioned...Yeah...Uh, when Lust died, when Sloth died (of all people...), when I was afraid Mustang had died, when Scar died, when the snake chimera whose name I can't remember died, when Ed died, both times...Eh...Yeah, pretty much the last fifteen episodes made me cry for one reason or another...Along with random moments throughout the series...
TRC: When Sakura woke up and didn't recognize Syaoran and [spoiler=Manga Spoilers]Syaoran stepping into Kurogane's childhood, and Kurogane's confrontation of Fye. Those hit me pretty hard[/spoiler]
Bleach: [spoiler=major manga spoilers!!]Almost all of volume three, particularly: Tatsuki's description of Ichigo before and directly after his mother's death and Ichigo's desperate and reckless attempt to defeat GF once he figured out that it was his fault his mother died, Kaien's story, re-reading volume three after reading Kaien's story and realizing what Rukia must've been thinking/afraid of, when Rukia was about to be executed (There was a horrible, horrible moment when I thought she would actually die), when Ishida found out that his grandfather died directly because of Mayuri's interference, Aizen's betrayal to Hinamori, Hitsugaya finding Hinamori, Renji pleading with Ichigo, Byakuya's reasoning behind not saving Rukia/Hisana's story, Ururu being skewered by Eilforte, and in the most recent chapters Hinamori's plead to not kill Aizen, even after all he's done to her.[/spoiler]
Naruto:
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Gaara's history, Sasuke's history, the entire Haku/Zabuza relationship, the Kakashi Gaiden, not to mention any reference to the hell of Naruto's childhood, when I thought that Neji and Chouji had died, the entire Sasuke vs. Naruto fight...
Cowboy Bebop:
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Faye's past and Spike's death
I cry so much over anime. It's a little pathetic...
Those are just the moments that I can think of right now...