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Tear Jerker: Mushi Shi
The second episode. It's the story of a little girl, Sui, who has a strange and apparently incurable disease in her eyes, causing them to become extremely sensitive to light. Despite seeing every doctor her family could find, it reaches the point where even the tiniest amount of light caused her excruciating pain, and she's eventually locked in a storage shed with no windows. Biki, her cousin and Only Friend, visits her every day, brings her food, and plays with her, despite his mother's fears he will contract the disease himself. In his words: "They said it was for Sui's own good that they left her here, but to me, it seemed like they were giving up - like they were abandoning her."
One day, Sui tells Biki that she already knows the cause of her disease, there are Mushi, mysterious beings and the focus of the series, living in her eyes. She also tells him that when she closes her "second eyelids", she can see a river of light in the otherwise pitch-darkness. When she tries to get closer to the river, a mysterious man warns her not to, that the river isn't safe to look at for long. Meanwhile, Biki's mother's worst fear is realized, as her son catches Sui's illness. The next day, when someone comes to bring Sui her food:
Sui: Biki? Biki? What's wrong?
Biki's mother: Biki...won't be coming back. He's caught your illness. I know you didn't mean it...It's not your fault. It's my fault for feeling sorry for you.
After Biki's mother leaves, the light from the river begins to shine brighter around Sui, indicating that she's dangerously close to it. She begins to sink into the light, all the while repeating in an anguished whisper: "Biki... Biki... I'm sorry... I'm sorry..".
Where Sea Meets Man. Imagine sitting on a beach for two years, watching the sea for some sign of your disappeared wife even as it's clearly hopeless that she's alive. One of the anime's saddest tracks plays when the man finally receives closure about her death.
The final chapter, where the young, human mountain-master gives up her life to save Ginko. At the same time she's returned to the life stream, her older brother (who never gave up on her even though she was a weird kid and then went missing for over ten years) hears the sound of bells all over the mountain — the same bells he heard when she was conceived, and knows that she's no longer among the living.
In Clothes That Embrace The Mountain, we are introduced to a man named Kai, who wants to become an artist (much to the disapproval of his father). He finally does leave his small town and, gradually over the course of ten years, does make it big as a successful painter, but after falling into a rut with his work orders piling up, he decides to take a vacation and return to his hometown for a visit. He returns to find the entire town had been buried in a landslide three years before, killing his father among many others. One of the few survivors left, his aunt, reveals that after the disaster his sister sent him a letter requesting help - a letter Kai had burned in the fire without even looking at it, assuming it was yet another work order. It's also revealed Kai's sister died giving birth a year after the landslide, and her young daughter, Toyo, is developmentally slow. Kai decides to raise the girl himself, despite his heavy workload.
The last chapter of volume 9: We learn that, because of the tokoyami mushi, Ginko doesn't remember any part of his life from where Nui was involved and before. Nui was the woman who took Ginko in when his own mother died and explained to him what mushi were for the first time, and she was the most critical event in his life that made him into who he is today. Ginko doesn't remember how he began his lifestyle as a mushishi in the first place. He knows less about himself than the readers do, which isn't much.
Aki, the Mama Bear from Cotton Changeling. All she ever wanted was a child, and instead she got afflicted with a mushi that not only produced clones of itself to look like actual children, albeit with strange characteristics such as green hair and abnormal growth rates, but it actually killed her normal fetus in the womb in order to do this. Once Ginko uncovers the truth about the mushi, they try to force themselves into hibernation and disappear by burning down the house with everyone inside. Everyone survives, but poor Aki is left a sobbing wreck in the arms of her husband as they sit, childless once again, outside the burnt remains of what was once their home.
The ending to The Pillow Pathway. Kin's dreams weren't prophetic at all - in fact, the mushi he was afflicted with were making anything he dreamed into a reality. Anything. And he's never going to be completely rid of it. By the time he figures this out, though, he's already had a dream that's wiped out everyone else in his village. He ultimately loses his mind with guilt, and stabs himself.
Episode 3 of Zoku-Shou. Basically, the young man afflicted with a mushi that drops his body temperature and causes it to perpetually snow around him isn't making any effort to take care of himself because he's deeply grieving the sudden and tragic death of his little sister, who fell into the town's frozen lake and died in his arms. Partway through the episode he nearly dies due to walking out onto that same lake and falling through the ice; he only survives because of the mushi snowfall. The episode ends on a hopeful note, but still...
The episode/chapter "Azure Waters". The young boy was so closely intertwined with the water mushi he was afflicted with that it was impossible to separate them, and it took over his body completely, resulting in him literally evaporating in his mother's arms. As it begins to rain, the bereaved woman takes comfort in believing that her son now exists everywhere as a force of nature.