Aftermath of Lee vs Gaara fight, Gai's speech to Lee, Zabuza's final act And words after Haku's death, Jiraiya's death and Naruto crying on the bench, Neji's death and Lee crying for it, Kushina's last words to baby Naruto.
Never cried over the manga but the anime is a different story.
Zabuza's death
Jiraiya's death and when Naruto found out
Asuma's death and seeing Shikamaru's reaction
At the end of Road to Ninja when Naruto returns home and ses Iruka.
Kushina and Minato's goodbye to Naruto
Sai and Shin flashback
That's all I can think of now. I'm overly emotional *sigh*
Forgot about this! Gaara's speech moved me, when he starts talking about how Naruto cried for him as an enemy, it made me realize how much of an effect Naruto truly had on Gaara. Gaara, a very young man managed to rally a whole army by telling them how much he wanted to protect his friend. That's some deep shit man
-When Pain was killing everyone (including Jiraya).
-Neji's death was sad.
-(ANIME ONLY) When Edo 3rd Raikage's fight was hella short, lame, and didnt really show the Anime watchers how invincible he is... Oh well.. We manga readers know.
Zabuza's death,Itachi's death,jiraiyas death, when naruto came back to the village after he fought pain and he finally became acknowledge by the entire village
I cried when Obito died and when Gaara was talking to Kankuro in a flashback in the beginning of Shippuden about not wanting to be seen as a monster, having a goal, wanting friends, and wanting to be accepted.