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.