Final Fantasy IX. Just... everything to do with Vivi and Quina. Those to characters cemented IX as my favorite in the series after initially writing it off as inferior to VII and VIII. While those games have some great narratives, Vivi and Quina both do such a great job of exploring what it is to be human, in their own beautiful and heart rending ways.
The entire experience of Outer Wilds.
So many parts of Persona 3, 4, and 5, but especially 4.
Here's a weird one: Starflight on Genesis. Not so much because of the story or content, but because I played this game so much with a friend of mine in middle school, and had all but forgotten about it. I was playing through some old Genesis games a month or so ago, and started this game up. As soon as the title screen came up, a flood of memories washed over me and took me right back to 1992. Bawled like a kid for about ten minutes as I realized I had an awesome friend that I had basically completely forgotten about.
Ah, yes, everyone's favorite Dorito flavor, Dick Kicker.