The "Reaper of the Thirteenth Step" chapter. After Aya spends two months outrunning Izanami in his game of tag, the final day is the day of the school marathon, where Izanami will be running and chasing her the entire time. Aya runs as fast as she can...and not only outruns him to the very end, but comes in first place in the marathon, as all the running she did earlier has given her practice. After she collapses at the finish line, Izanami helps her up, congratulates her on besting him, and suggests she take up track and field. The chapter ends not only with Aya finding new meaning in her life, but she and Izanami develop a sort of master-student relationship with Izanami wearing a sports coach uniform instead of his reaper robes, and telling Black Tea Gentleman to stay far away from Aya, as she is now under his protection.
The "My Best Friend" story. Tomoko forgoing the chance to be resurrected and even pretending to despise Michiru, so that her friend would live her life happily and get over Tomoko's death. Also qualifies as a tearjerker.
"Before the Spider Lilies Bloomed" gives us Higanbana's backstory, which starts out surprisingly heartwarming... before moving into Tear Jerker and Nightmare Fuel territory. We see that Higanbana was once an Emotionless Girl who killed only to survive, but began to develop emotions after meeting a bullied student named Shūichi Arimori, who had a very philosophical view of emotions and was Wise Beyond His Years.
Though her Start of Darkness is a terrifying and depressing story, "Before the Spider Lilies Bloomed" ends with Higanbana reuniting with the adult Shūichi, who still remembers her and reaches out to her despite being blind now.