Nanako helping Johnny once he fell down the stairs, simply because he is family.
Chie and Yosuke STILL defending Johnny from his Shadow, despite being shown and told what he really was like and what he feels. Simply because they can't leave someone to die alone, even at the risk of their own personal health.
Johnny, truthfully and politely asking if Yosuke is okay and being glad that Chie is alright as well after the battle with his Shadow.
Yosuke willing to try and have his Shadow focus on him rather than harm Johnny anymore.
Johnny not holding it against Yosuke for the thoughts his Shadow revealed, made even better when the thoughts revealed were that Yosuke only hung out with Johnny initially because he probably did not have any friends, and that Yosuke got a momentary kick out of seeing Johnny get taken down a peg in his memories.
Yosuke admitting all of Chie's faults, but also stating all her good points immediately after and calling out her Shadow's bullshit.
Chie wanting to start over with being friends with Johnny after her Shadow revealed that she wanted him, Yukiko, and even Yosuke to look up to her and make her feel special. Made even better when Johnny accepts, albeit he does make a snarky comment about her way of "starting over" via re-introducing themselves and shaking hands being cliche as all hell.
Chie reuniting with Yukiko. Them hugging it out and the relief Chie feels just melts your heart.
Johnny taking Dojima's skimping out of the planned Golden Week vacation... rather poorly. And rather than allowing Nanako to sulk and feel sad by denying her plea of going someplace on the third, he accepts it.
Johnny admitting to Gyro that not warning him about the killer would not sit right with him. Keep in mind that the original plan was just to spy on Gyro from a distance, and Johnny rationalized just telling Gyro because hiding would make both him and Yosuke look stupid.
Johnny and Chie finally making up after several chapters of bickering and arguing. The fact that they talk heart-to-heart about their problems and doing so allows them to understand one another better while also repairing their Social Link makes it even sweeter.
Johnny willingly putting himself in danger to protect everyone. Keep in mind before this Johnny wouldn't have done something as selfless as this, so this shows how much he really cares for Gyro and the others.
Yukiko and Kanji having a heart to heart talk where Yukiko comes clean about intentionally avoiding Kanji until recently, and Kanji accepting her apology because she bothered to be truthful with him.
Most of Johnny's interactions with Nanako qualify. Despite his initial grievances towards taking the role as an elder sibling. He goes out of his way to make sure Nanako is happy even when Dojima's not around.
Gyro cheering up Yukiko with one of his lame jokes when they return to Yukiko's Castle. Due to her finding the jokes actually funny, she laughs and it dispels her worries about returning to the area.