The immediate aftermath of Chapter 50. The pain Yukimi is obviously going through can be rather wrenching to read - the same goes for Miharu's reaction, especially his Not So Stoic breakdown. "I didn't want to erase that person's existence... because I wanted us to live together... so why did I choose this...""If that person's memories or remembrance were left, I would surely... not be able to live..." And then he claws at his throat. And bursts into tears.
The final chapter of the manga. The color pages in the middle of the chapter with Miharu finally reuniting with Yoite are just plain heartwrenching.
This troper hasn't even seen the chapter in question but teared up just now by reading that spoiler. That's effectiveness.
Raimei's reaction when Kouichi dies. And on that note, Shijima's last words to Miharu:
Shijima: Take care of granny.
The second ending of the anime, which features Miharu and Yoite doing cute things like sleeping on each other's shoulders at a train station and holding hands in a grassy field, all set to a mellow, nostalgic-sounding tune. On its own it's very sweet, but in the context of the show it becomes heartbreaking.