In spite of herself, Haruhi smiled. It wasn't quite what she originally had in mind when she was looking for people who were different from 'normal'. She'd thought initially that playing with time travelers, aliens, espers, sliders.... Well, she'd originally thought that having fun would involve using their powers a lot.
Well ... it wasn't what she had been looking for. But maybe it was what she had wanted, anyway.
Pretty much any time the story is told from Imouto's perspective. It shows how much she really does care about Kyon, such as being grateful to Haruhi for making Kyon as popular as she knew he could be, although being worried about losing her older brother to his friends. The best is probably this conversation with Kyon's father:
Imouto:(answering who 'Haru-nee-san' is) Haruhi! You haven't really met her, though. She's the one that fixed up Kyon!
Kyon's father: Fixed up Kyon? When did he get broken down?
Imouto: In middle school. He lost his smile for a really long time. Didn't you notice? But it doesn't matter — Haru-nee-san made him find it again!
Not even his parents had realized it, but his little sister did.
Kyon's sister knew for some time her brother was a hero, so when Kyon told her he just raided a Dark General's note Fujiya Masao base and beat up him and his henchmen it was interesting to know but kind of expected. However, after she learned the Dark General wasn't killed or sealed away * forced to cut his pinky finger or to kill himself because Kyon ordered him to redeem himself note never work with voyeur pictures bought off high school students again she felt especially proud of her brother, giving him a powerful hug and told him he was a good hero.
In the aftermath of the SOS Brigade anniversary party Haruhi admits Tsuruya being worried about the Marry Them All scenario she's planning for the girls in the brigade and Kyon and how she isn't sure if she could go on with this without Tsuruya, Mikuru, Yuki and Kanae's support. Tsuruya's answer? "It doesn't matter if you could or couldn't! You don't have to!"
And that, Haruhi realized, returning her friend's hug, was what really mattered.
"Thank you ... Nii-san."
"I categorize you as a friend."
Yuki's discussion with Rika.
Rika: "Nagato-chan, might I ask what your intentions with my nephew are?"
Yuki: "For the duration of his time in Hinamizawa I have been asked to ensure his safety; I will continue to do that, unless he should ask otherwise."
Rika: "I meant beyond that."
Yuki: "The future is ... uncertain."
Rika: "That doesn't answer my question. I mean, what do you want with him?"
Yuki: "That which is uncertain; a future."
This short exchange between Yuki and Kuyou after Kyon kisses Kuyou in Chapter 57:
Kuyou: "Where is, 'the special hell'?"
Kuyou: "I must find it so that when he goes there, I can go with him."
He didn't let himself kiss her back reflexively; he didn't want to do things like that without thinking. If Haruhi and the others were going to be going so far, he had to pay it back. No absently putting his arms around someone, or kissing them just because they were close. From that day forward, he promised himself, everything — all of it — would be intentional. Not just any girls — but the girls he was going to try and be with — and no one else.
Rika's horror that Kyon immediately believed her. What could possibly have happened in Kyon's life that he believes her immediately? The heartwarming is in how Kyon's weirdness is mostly just hanging out together peacefully.