I'm sadly tender for emotional scenes involving loss of loved ones or family, whether permanent or temporary.
One of the things that made me cry that I haven't heard about anyone else that watched it cried to, is the part of the second episode of FMA: Brotherhood where
Edward screams to give his brother back, and puts the blood seal on the armor.
As for anime/manga I can think of that made me cry...
FMA: Brotherhood, I actually already told you guys about that above... >.<
Tonari no Kaibutsu-kun, I actually forget what made me cry, because I looked over and couldn't find the same thing again, to cry about.
Inari KonKon Koi Iroha when
Uka-chan realized that Inari no longer needed her, she cried and I cried seeing her cry
Tower of God when
Rachel betrayed Baam I was soooo mad that I cried
Steins;Gate, When
Okarin said his last goodbyes to Kurisu and reset the world line to how it was, I cried
Golden time, when
he told Koko the truth about his feelings for Linda, and her reactions and the way he acted, I cried.