Jay seemed so sad and frustrated until Rhus showed up.

And I also note that Jay and Acy's little argument in one of the missions in the TOS (I think it was the Aria one) that ended up in the two being seperated on different sides of the Bridge for a night was pretty sad, too.

These aren't really tearjerking, but they're pretty sad.

"A low, almost subsonic, buzzing could be heard. Oh no! cried Makes-Things. Get a phaser, Agent Cameron! Then he screamed. Tawaki heard a sickening crunch and a thump, and the connection ended.
Makes-Things? Makes-Things? MAKES-THINGS? S---. "

There's also Nyx choosing to leave with Dassie, the Building of the Tomb of the Unknown PPC Agent, and Jay and Acacia's retirement.

...the death of Elanor Laison, off of the top of my head.