Oh yes this is going to be fantastic. My nominations (in no particular order):
Undertale - Heartache
I also love ASGORE, and Megalovania, and Battle Against a True Hero, but Undertale’s first boss theme might still be my favorite. It’s understated in a way that fits its moment, when you still don’t quite understand the stakes of the journey you’re about to play, and it’s filled with a kind of solemnity and quiet power.
Shovel Knight - The Defender
This theme is great for two reasons: 1) it comes at an absolutely off-the-wall moment in the game, when you rematch a previous boss except now that boss can fly and summon meteors and shoot massive fireballs in an incredibly satisfying and well-tuned fight, and 2) it’s a partially-remixed, more frenetic version of the theme for the game’s first level, and it really carries this sense of progression and knowledge of how far you’ve come as a player since them.
Pokemon Mystery Dungeon: Explorers of Time/Darkness/Sky - Primal Dialga
This one is just so different from typical final boss themes—it’s still driven and climactic but the the instruments the composers chose also give it this sense of peace and clarity that really fit the end of this (extremely underrated) game. One of my fondest gaming memories is the first time I played this fight, and the first time I heard this song.
The Legend of Zelda: Breath of the Wild - Beast Ganon, Phase 1
As you can probably tell, I’m a sucker for leitmotifs and callbacks, so when the true final boss of Breath of the Wild ended up being a remix of the game’s absolutely incredible main theme mixed in with signature riffs or music from about four or five previous Zeldas (Ocarina of Time, Wind Waker, Twilight Princess, among others), I dissolved into a puddle of my own happy tears.
Pokemon Gold/Silver/Crystal - Champion’s Theme/Red’s Theme
Replaying Silver on my 3DS for the first time in probably a decade has made me remember just how good that generation’s music was, and this piece is the capstone. That moment of finally finding Red at the top of Mt. Silver and hearing that moment of total silence before this theme started playing easily ranks as one of my favorite moments in a series I’ve poured something like two or three thousand hours into.