Platypus Comix/Tear Jerker

Hillary Clinton realizing that even though switching bodies with Mulberry in "Obamadramarama" gives her a second chance to rise to power, refusing to return to her own body will disconnect Hillary from her daughter.
Mulberry finally letting the news of Brittany Murphy's death sink in in "Murphy's Lawn".

Amara endures a number of depressing incidents in "Freewheeling", especially when she discovers that the time she became a popular trendsetter was All Just a Dream.
- Peter Paltridge boasts in the Keiki archive that people called this the best comic he made up to that point, but doesn't explicitly say why.
Darcy's rant about the media's romanticization of vampires in "Twilight Princess" includes a lament about the fact she can never have a romantic relationship with the mortal Beefer.

Arguably, the part of "Princess Pi vs. The Totally Nazis" when the Totally Nazis' ceaseless insults appear to push Pi over the Despair Event Horizon.
"Princess Pi vs. Cerebus Syndrome" plays most of Pi's overly grim stories for laughs, but the story of the death of her mother feels genuinely sad.

"True Believers":
- Peter Parker equating the thought of losing Mary Jane with the anxiety previously felt before Marvel released The Night Gwen Stacy Died.
- Peter and MJ preparing for the moment when Joe Quesadilla will split them up.
- The part when the fact that Death Is Cheap in the Marvel Universe leaves Spidey doomed to eternally suffer the loss of MJ.
- MJ's sacrifice.

Peter Paltridge's unending suffering in "Kellogg Middle School: The Happiest Place on Earth".
The "Concept Unification" video in "The Chuck E. Cheese Story", detailing the transformation of a Showtime Pizza restaurant into a Chuck E. Cheese facility, includes a warning not to watch it because "it's too depressing".