This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Vampire Knight
When Ruka comes to Akatsuki in tears because Kaname is being a Magnificent Bastard (which he usually is) several people felt sad, because Ruka is usually shown to be a bit of an emotionless bitch.
Another Aido-related example: when Kaname kills Aidou's father.Her reaction was heart-wrenching as she watches the man she's pledged to kill a man. And a good one at that. And Aido's face...
Yet another Aido-related example. After Kaname kills Aido's father. Aido is in a room sulking and Zero comes in to tell him that he can leave if he wants to or can ask the Chariman for details. Aido proceeds to break down saying something along the lines of, "If I'm tormented by hatred for Kaname-sama and his sister too Yuki, No I won't become like that, I won't become like you, no matter how hard it is right now." Zero then walks away, with his signature emotionless face.
Yuuki and Zero's separation after the Rido battle. No moment in the manga had a bigger emphasis than when they team up to fight Rido, Zero pointing the gun at Yuuki after Rido's defeat, then proceeding to pull her in for a violent hug after Kaname's left and making an Anguished Declaration of Love before kissing her in a dramatic "falling" panel, then ending it with Yuuki proclaiming she will always run away from him if it gives him a reason to live. Couple that with the cover Hino drew of the two embracing in the middle of a blizzard with Zero's vines wrapped around Yuuki's Artemis and the caption "At the very utmost ends at this world... where we shall never again be together." Hino's own comment to that cover was that she wanted to make it feel like time itself had stopped for a moment. Just... awww...
The end of chapter 88, where Yuuki attempts to erase Zero's memories of her. Zero's desperate face while telling her stop and Yuuki's devastated face while telling him she's sorry might be the first real competitor to chapter 46 in terms of this story's tearjerkers.
Chapter 40/Vampire Knight Guilty episode 11, i.e. Ichiru's death? Zero has lived for about 5 years believing his entire family was dead, only to be reunited with his twin when said twin was clearly out to see him dead. In the lead up to the climax in the chapter/episode, you're shown how close they were in the past and that's already heartbreaking enough especially when you're first led to believe that Ichiru wants to kill Zero (shooting him with the Bloody Rose anyone?) Then, you realise that actually, despite everything, Ichiru's love towards Zero won out over his hate and he's come to force Zero to eat him so that Zero won't fall to Level E, will be able to live up to his destiny of being the strongest hunter in history and ultimately will be able to fulfill his goal of killing Rido and hence protecting Yuuki and still be alive at the end of it. Zero already hates being a vampire, and now he's just been told by his dying twin to deal the final blow to said twin. The anime even makes him cry as he's preparing to bite Ichiru.