The flashback to The Graveyard Scene with Kanone and Eyes; technically sad, but damn, those kids are cute.
In the manga, Ryouko and Kousuke holding hands in the hospital.
In the manga, Madoka hugging Ayumu and telling him about human warmth... and prompting him to later hug Hiyono out of the blue, shocking her out of her wits.)
The manga epilogue, which doubles as a Tear Jerker.
