Ibara immediately drops her problems with Oreki's version of the student film when she sees how horrified he is that he could have messed up someone else's film. It doesn't stop the Heroic BSoD he experiences later, but its quite considerate given how much they prefer to snark at each other.
The way Tomoe acts with Oreki when she returns from overseas, especially in the OVA. It's not for long, and it's relatively subtle, but she clearly loves her little brother, even if she can't resist meddling in his life (and it's usually for his own good).
This exchange from episode 15—
Mayaka: Oreki, do you want to catch Juumonji?
Oreki: I don't really care, but Chitanda got curious. I can't avoid it.
Mayaka: You should just ignore her then.
Oreki: The problem is that she's not someone I can ignore.
At the end of episode 17, Satoshi and Ibara have both seen their own abilities out-shined by others. They share a half-hug.
Just as Satoshi begins putting on his Jade-Colored Glasses, Mayaka gently tugs on his shirt, reminding him that there's still someone who will never think less of him.
Episode 19, where Eru and Houtarou sit and talk together over a problem-solving game of what a school announcement was about. At the end, Houtarou smiles, with no snark or effort, for the first time in the series.
Episode 21 has a fair bit of tearjerker. Satoshi ruins Ibara's Valentine's chocolates and Chitanda feels that she's to blame for them getting "stolen". The heartwarming part? Houtarou gets angry and confronts his best friend, calling him out on hurting Ibara and, indirectly, Chitanda. He cares enough for both girls to get legitimately angry, something that happens incredibly rarely.
At the end of episode 22, Houtarou inadvertently considers indirectly admitting his feelings to Eru, and the series ends with both him and Eru enjoying the sunset and cherry blossoms together.
This, from the finale:
Oreki: It's getting cold.
Chitanda: No— it's spring now.
Remembering Oreki's schpiel at the beginning of the series of a "rose-colored high school life", you can tell that he's definitely changed and embraces the rose-colored life; wrapping up the series with Book Ends.
An easy-to-miss one, but even Irisu gets a heartwarming moment in the last episode. Houtarou gets suspicious when she asks his opinion on why the procession took a different path than it was supposed to, but Irisu replies that she was honestly curious. She may be a Manipulative Bitch most of the time, but Irisu can actually be somewhat friendly when she doesn't have a goal in mind.
