This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / The Magic School Bus
When D.A. loses her book bag and self-confidence in in "Blows its Top".
Keesha's Heroic B.S.O.D. and subsequent ten-minute retirement in "Gets Ants in Its Pants".
The bus almost gets flattened in "Revving Up". The music does not help.
Tough girl Wanda actually cries in "Holiday Special" when her favorite toy from early childhood, which she'd intended to give away to other children who otherwise wouldn't get Christmas presents, gets mulched up and melted down into plastic pellets instead.
Arnold, who's responsible for accidentally destroying her toy, feels guilty. What's worse is that the scene comes right after he squees that she likes the gift that he got her, not knowing she was the recipient.
Also, in the same episode, the Bus hitting itself with the Recycling Ray, since it has to hit everything that's made of recycled materials, even itself. The fact that it's still smiling just makes the scene all the more unsettling.
The episode wherein Wanda gives up her pet "Bella". For any kid, this can be tough to watch.
In the butterfly episode, Janet mocks Phoebe's suggestion of making butterflies the school mascot but that's not the Tear Jerker. The Tear Jerker is when Janet suggests that Phoebe is sabotaging them because they're playing her old school. The rest of the class immediately turns on Phoebe, to her obvious fear and confusion and despite the fact that before Janet pointed it out, the idea that Phoebe might have divided loyalties hadn't occurred to anyone. Were they a little older, I'd wonder if she'd need a suicide watch after that.