Metal Gear Solid 3: The act of killing The Boss didn't quite get me, but the salute over her grave at the end did.
Elite Beat Agents: You know what level. The fact that this game is here alone is basically a spoiler.
Persona 4: When Nanako dies and Dojima just keeps screaming for them to give her back.
Danganronpa V3: Case 4, when Gonta is just sitting there sobbing as he comes to terms with what he did got me, mainly because of the voice actor's performance as he's barely audible when he says "OK".
Outer Wilds: Both the base game and the DLC did this. The ending around the campfire into the end of the universe as the music swells is just masterfully done. And then for the DLC, it wasn't until after everything and I was stuck in the simulation wondering what to do when I started thinking back on everything and realized the gravity of what just happened.
Tetris Effect: No spoilers here. I just played it in VR and had total sensory overload as the lights and the song overwhelmed me.
There are probably a few others, but I can't remember them off the top of my head.
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Xbox GT/PSN name/Nintendo ID: TatteredUniform http://www.scuffletown.org/wp-content/uploads/2010/05/tRBE1.gif