Episode 5. Similar to the aftermath of said Episode 3 but less of an impact, Kirino makes up with Ayase, and she asks Kyousuke to play a game with her right there in the family room. With a bright smile, she says, "I'll beat the crap out of you."
Volume 2 of the light novels: When it seems like Manami is avoiding him, Kyousuke becomes worried that one of his joking comments about Manami's plainness may have actually gotten to her. Putting aside her animosity for Manami, Kirino suggests that Kyousuke give the meganekko a gift to make amends. Kyousuke does so and waits for Manami outsider her house for two hours just to give her the present (a pillow). When she finally comes out, it looks like she wants to avoid Kyousuke so he has to grab her hand, begs her not to run away, and asks her why she's avoiding him. It turns out one of his comments did get to her, but not the one he thinks. The day after they met Ayase, Manami decided to trim her hair, but she didnít do it very well and that meant she had actually changed. Since Kyousuke always told her that she was a reassuring constant in his life and hopes she never changes, she had been avoiding him so he didnít hate her. He assures her that she'll always be his precious friend and the misunderstanding is cleared up.
Episode 11. Kirino finally thanks Kyosuke for all that he has done for her. This troper almost cried Manly Tears with Kyosuke during this scene.
The Entirety of Episode 12. Truly a "Good End". But to point out those that'll warm you up:
The start of the episode, no less, where Kirino is treating Kyosuke kindly. YMMV if this counts as a CMOH, though, as it appears out of the blue, mostly as foreshadowing.
Kirino revealing that she has to leave for America and wouldn't be back till High School (Read: Many, many years.) and Kyosuke keeps insisting that she should go, even till the very end, with Kirino hoping the whole time that he'll tell her not to.
Kirino is 14 - it would have only been one year - it's still a fairly long time though
It's hinted that Kyosuke bled a lot after Kirino headbutted him in the chin, and she put him back in his bed and spent all night cleaning up the blood and treating his injuries.
Episode 14. A few days before the deadline, Kuroneko's game gets stuck in production due to several bugs and crashes, and gets told that she won't make the deadline. She walks out of the room, but not for the reason Kyousuke expected: she actually sets aside her animosity towards Sena and begs her to help fix the bugs. Kuroneko even makes a little speech about how it feels good to have someone to rely on. And Sena's response?
Sena: "I won't help you. We'll make this game together."
Episode 15: Kyousuke goes to America in order to find out why Kirino wants him to throw away her collection. He tells her that everyone is worried about her, but she says she can't be dependent on everyone anymore and she starts crying. At that moment, Kyousuke lets out his true feelings and tells her he is lonely without her, and that everyone else is an excuse to be in America, and he wants her to come back with him. She does.
All of Kuroneko and Kyousuke's interactions in the second season as they come to terms with their feelings for each other. Special mention goes to the end of episode 7 where they both reveal that they stayed up all night long thinking about each other and how to go about being a couple. Kuroneko ended up filling a notebook with her most embarrassing desires to get it out of her system, and Kyousuke asks her to pick something from it anyway, because he wants to do the things that she wants to do.
Episode 9 of season 2. Shortly after Kuroneko breaks up with Kyousuke, then disappears and refuses to answer his calls or texts, he ends up crying to Kirino and asking her for advice. Kirino tells Kyousuke to turn around briefly, then immediately puts him in a chokehold. But shortly afterwards, she gives him a hug from behind, and seems to genuinely care about the predicament he's in, despite being extremely uncomfortable about the whole thing in the previous episode. She then goes out of her way to help him, much like he's done for her several times before.
Ayase's confession to Kyousuke at the end of episode 12 of season 2. Actually, that entire exchange with just the two of them is the cutest, especially Ayase's farewell, complete with a kiss on the cheek. May count as a Tear Jerker for some as well.