They all contain spoilers:
Mother 1
The talk and fight against Giegue/Giygas at the end of Mother 1 hit so hard. You can’t battle your way out of this one; you sing your way out, presumably driving Giygas mad in the process. I still think about this on the regular and I wish it were clearly referenced in Mother 2, because as far as I can tell, it is never directly brought up. Mothers 1 and 2 occupy a weird space for me wherein I think of Mother 2 as being like the NGE Rebuild movies, because Mother 2 hits a lot of the same beats as Mother 1, but it feels very clear to me that what’s happening is taking place after the events of Mother 1.
Anyway I’m really emotional about Giygas.
Final Fantasy IX
Beatrix just rolls your party at the end of Disc 1 and I think about it a lot because I love Beatrix but also I really like it when these games use combat as a means of storytelling.
Final Fantasy X
idk something about having to fight your own aeons at the end of X really fucks me up.
Racing Lagoon
It is less the exact encounter that happens with Kyoji Nanba on Night 5 and moreso the fallout of it that really gets me. This game was not afraid to just kill these boys. I can’t really look at this encounter the same again.
Metroid II
The fight with the Metroid Queen would not be that big of a deal…except that immediately afterward, that egg you saw finally hatches and the baby Metroid within has attached itself to you. It loves you on sight, even though you just exterminated every other member of its species. You are forced to reckon with what you have done in the long, quiet climb out of SR388 back to your ship. It gives this extra weight to subsequent plays of Metroid II that remind me every time that, yeah, I just killed an entire species. That baby about to hatch is the last one ever, and it’s going to sacrifice itself for me soon.
this is also why the remake is inferior, because it robs the player of this moment in favor of a dumb fanservice fight
Star Fox 64
The fight against Andross at the end of Venom II is important for me historically because the first time I reached this fight, I actually had a panic attack and couldn’t finish the game. I was maybe 9 at the time. If I’d known the word “anxiety” maybe my life would have turned out differently. But notably, I beat this boss on another attempt at that age and was so grateful I could get past the anxiety to claim victory.
Honorable mentions go to the Pure Vessel/Nightmare King Grimm fights in Hollow Knight, the Roxas fight in KH2 (Shimomura is criminally underrated), and the Lord Ninetails fight in Ōkami.