Heartwarming Moments: Takako Chigusa's death scene, in Hiroki's arms. Despite having brutally murdered a guy moments beforehand (admittedly, in self defence), she's the object of nothing but sympathy from the audience in her final moments as she begs God for just a few more moments in the world with her best friend and true love. In the manga, it's especially heartbreaking since she has flashbacks from the time when she and Hiroki were kids together.
Shinji and Yutaka's reconciliation in the manga had a healthy dose of this, until Kiriyama droppedby.
All of the manga's flashbacks with Shuuya. Especially the one in volume five.
Although there are very few, this one stood out to me. "Once again, 2 students remaining. But now they are among you."
Near the end of the movie, Kitano tells Noriko to shoot him. She fails to do so, so Kitano starts to shoot. Shuya ends up killing him before anything happens to Noriko. Noriko wouldn't have died anyway, because Kitano's gun was filled with water... He never meant to hurt Noriko in any way. Also doubles as a Tear Jerker.
In the Manga, any moment between Mimura and Yutaka. To say Mimura has the patience of a saint is a huge understatement.
Among the biggest ones being when Shinji accidentally kills one of their classmates. Yutaka snaps, calling him out on it and damn near losing his trust in Shinji. In the end end, however, he decides to forgive Shinji and stick with him, due to how patient Shinji had been with him, despite all of his screw-ups. This display of faith was enough to bring Shinji to tears. Sadly, this is almost immediately followed by Yutaka's death, which came completely out of nowhere.
There's a flashback scene in the manga where Shinji is visiting Shuuya and Yoshitoki at the orphanage and is on the floor playing with some of the younger kids. Doubly heartwarming when you remember that in an earlier panel, Yoshitoki was embarrassed to admit he lived in an orphanage.