Entirety of Shirou's treatment of Akitsu. He was on the run, didn't trust her race one bit and was going out of his way to avoid them. And then he met broken, almost naked Akitsu sitting lonely in the middle of the park. Old habits kicked in and without a second thought he took her in and accepted her as his Sekirei, something Akitsu thought would never happen. And it only gets better from here, every time they interact Shirou makes sure if Akitsu is alright and comfortable. He is even determined to confront Miya about No-Pets Rule because Akitsu wants a doggie.
Shirou's thoughts prior to that moment are a CMoH on their own:
Shirou:Even if it was only a chance, even if it was one in a million, even if my assumptions and guesswork were based off hazy incomplete evidence and possibly completely unrelated coincidences, it was still a chance. And Akitsu deserved that chance. She had tried, so damn hard it was enough to make me misty eyed, to live past her condition. She had done everything she could, more than probably any other Sekirei in the plan, to be the best Sekirei she could, to be the most loyal and worthy person she could. Despite her fear, despite the hardship that she had been through, despite the shame she no doubt felt, Akitsu had given her all to me. I hadn't known what my impulsive decision to accept her oath would mean to her, not when I had accepted it. Now that I did, it was my obligation, no my duty, to do everything I could to repay her loyalty.
Kusano's and Shiina's reunion.
In the Twenty Sixth Wing, Matsu and the rest of the Sekirei tell Shirou that he is not alone, and that they will help him even if it means fighting Magi. Even so, Shirou has a new dilemma, he realizes that his belief that has cultivated to what he became and what would eventually happen in his future (Dying Alone on a hill of swords) is the greatest fear of his own Sekirei.
Thirty Second Wing, the entirety of Chiho's recovery and the reaction that Uzume has.
Thirty Fifth Wing, Uzume announces that she's leaving and Shirou breaks down her reasons why easily. Later on, the two of them talk, alone and Uzume does something that neither Shirou nor Archer ever got in their lives for doing something similar in many situations. She said thank you for saving her from a bad situation. It might not seem like much, but for Shirou, it was enough to leave him speechless and it caps off the bromance that Shirou and Uzume had going with each other throughout the story.
Thirty Seventh Wing. Despite all the awesomeness that's going on, there's one point that sticks out. Shiina asks Shirou if the older man approves of him. Despite the fact that Shirou admits that he killed Higa, stormed the fortress and Yukari was kidnapped, Shirou actually gives Shiina his blessing to be with his sister.
Fortieth Wing has a boatload:
Tsukiumi giving up her night in order to allow Rin and Saber to comfort Shirou. Remember, she lives on love, these two women are rivals to her, and it was supposed to be her first time.
Rin giving the Sekirei approval to be with Shirou because they can keep him from doing something to kill himself like he would in the past.
Rin and Saber both getting ready to put themselves into exile because, even though they found a way to bring Shirou back to the Clocktower without getting killed and experimented on, the Sekirei would be essentially experimented on and the species wiped out. Not to mention the Jinki. Rin openly admits she wouldn't care about them, but Shirou wouldn't let that happen.
In response, Shirou challenges Rin and Saber to a fight, knowing that if he wins they can return to the Clocktower without him.
There was no reason for me to go through with this match. The Path of the Shura meant measuring lives, and making the hard choices that would preserve the most of them. Even if it meant making Saber and Rin a sacrifice, it was the smart move.