Tear Jerker / With Big Shells and Wings

• Yellow's death. It didn't help that Red was so traumatized by the event that he became a sobbing, drunken wreck.
• Dix's death. Made all the more heartwrenching that he was a minor character who just earned his Mauve Shirt status and spent his final moments desperately trying to run away to safety.
• Steve's death. Like Dix, he was starting to get some Character Development when he's abruptly killed off—and right in front of his best friend Green too...
• The last two lines in Chaper 52, which turned out to come true:
  Henson: "We're not getting out of here alive, are we?"
  Larry: "No."
• After Eddard's village is burned down (and his mom is presumable killed), Eddard kills one of Trowzer's soldiers out of a fit of rage. Moments later, he finally breaks down sobbing and realizes how much he's lost.
• Eddard giving Hooktail a caustic "The Reason You Suck" Speech. Even if she did deserve it, Hooktail is clearly hurt by the Yoshi's words, and she has to force herself not to shed any tears.
• Chapter 54. ALL OF IT.
  • The first part has Bosley and Ned getting executed by Marcus in front of Kooper, Geno, and a bunch of other Yoshi rebels. Their deaths were so shocking that everyone (Kooper especially) went into a Heroic BSoD.
  • The second part has Larry dying minutes after Junior, Roy, and Wendy find his mutilated body. Junior and Wendy break down crying, but Roy tries to hold his tears back and go after Trowzer. But after Wendy and Junior stop him, Roy collapses to the floor and begins to cry alongside his siblings. It should be noted that up until this happened, all three of them hadn't shed a single tear, even when Iggy died.
• Bowser's last words are downright pitiful.
  "I was supposed to be the villain..."