How about when Miranda and Krory were welcomed by the Order?
The Noah all crying over the death of Skinn Bolic, and having a toast in his honor. Not to mention The Earl of all people crying when Skinn was first Noah-fied.
The twins too. When Krory manages to tear out a strand of Jasdero's hair he's in tears. Devit immediate response is to promise him they'll fix it and his look can only be described as fond. When Lenalee lands a punch later Dero is very worried for his brother.
When Krory finally wounds them enough to stop them from following his friends their first thoughts are about each other. Crazy? Damn straight. Deeply devoted to each other? Hell yes.
Cross: I can't laugh at Tiedoll anymore... Jeez...
For this troper, the scene where Allen 'plays' the Ark back into existence, along with all his friends, with the musician's song playing in the background and Komui's "when you get back" monologue playing in the foreground. The anime does it best
Chapter 199: Kanda actually thanks Allen. He even calls him by his full name instead of "bean sprout."
Chapter 204: Road protecting Allen from an attack, despite the attack being incredibly dangerous for her.
Chapter 206: Cross has to nurse Allen back to health so he doesn't die, being the host. However, even though Allen is merely being used as a container, Cross seemed to feel something for him. Empathy and guilt possibly. He complains at having to do house work and nurse Allen. But on one page when he wasn't nursing Allen, he was just sitting by his bed watching him with a sad look on his face. Then he goes on to try and get Allen to cheer up.
It's hinted Cross was lying when he said he didn't care about Allen. The scene of him being by Allen's bed debunks him not caring at all, along with him being upset and caring that Allen was acting like Mana. Mother reminds him of Allen's fate, and shortly after she does, Cross drinks and brushes his previous mood under the rug to drink. When he tells mother he doesn't care, she had a kind of sad or sympathetic expression on her face. Seems she may have thought or knew Cross was lying. Then when Allen shows up at her door years later, she thinks to herself that Cross did love Allen after all-otherwise he wouldn't look the way he did.
Chapter 207: The bonds with your many Nakama with whom you've laughed with and fought alongside...No matter how far away we are from one another, we remain connected.
Chapter 208: Kanda bidding Zhu good bye is both heartwarming and sad, but definitely more heartwarming. But what really got me was how he stated this time he would become an Exorcist by his own free will as Yu Kanda. That it was rather reminicent to the scene where Lenalee accepted her fate just added up (and also it doubled with adorable hilarity when he drank the Innocence from Lenalee's hand).
Chapter 214: In a flashback, young Nea's reaction to his brother Mana waking up out of a coma. "Boo." So goddamn adorable.
The nicer moments in the relationship between Kanda and Alma Karma, such as Kanda slowly warming up to Alma when they were kids and Alma dying in Kanda's arms.
Chapter 222 has a moment with Cross and Allen. One could argue 95% of the chapter was a Cross/Allen moment. We see Allen in Neah's consciousness. He wonders where he is, and what's going on. Cross appears and answers Allen's question, and tells him that he will disappear. He then goes on to tell Allen that he never wished for his death. He wants Allen to just rest in this place and live in happy memories until he disappears. Cross then tells Allen that he will stay there with him if he's scared, before mentioning that he is Allen's master no matter what, and remarks he used to clean Allen's soiled clothes and bed-sheets. Allen rejects the idea, remembering the promise he made to Lenalee, and says he will keep walking. Allen thinks the Cross before him is just an illusion born of his own weakness, but then says he was happy to see him again.
In a very messed up but still truly touching way, Nea hugging the Earl in Chapter 219.