Great mentions so far.
I might add most Ace Combat do an incredible job with this. The final mission is usually some dogfight or fight with some bigger aircraft so technical it's a sort of boss fight:
Playing it with headphones blasting at full volume, that part in the final mission when the enemy shield go down and after all the build-up the sequence at 3:14 in the song starts playing was one of the few moments last gen that gave me goosebumps
Slightly off topic but while the version in the game is great, the live recorded rendition from the Theatrical Orchestra concert of this song is incredible
I'm not big I to GaaS games and wasn't really sure about Honkai Star Rail until I approached this boss. It just kept building up to that insane vocal drop where I had chills all over.
It was like they poured every bit of money they made into that one fight. It made me remember just how much music and story is vital to a game for me.
Nier Automata is probably my favorite soundtrack ever. The Opera Boss had me in tears with just how beautiful it was with the attacks telegraphed.
Almost anything Yoko Shimomura puts out for Mario and Luigi and Kingdom Hearts boss battles.
Primal Dialga Boss theme in Pokemon Mystery Dungeon 2, such an intense final battle after a long emotional journey. Such a great theme.
Pokémon Colosseum Boss battles with the intense jazzy themes. Especially Mirror B. It helps that the game is actually challenging to set the tone.
Great mentions so far.
I might add most Ace Combat do an incredible job with this. The final mission is usually some dogfight or fight with some bigger aircraft so technical it's a sort of boss fight:
Playing it with headphones blasting at full volume, that part in the final mission when the enemy shield go down and after all the build-up the sequence at 3:14 in the song starts playing was one of the few moments last gen that gave me goosebumps
Idk, Megaman, Zelda, Mario, Bayonetta, Metal Gear Solid, Resident Evil, Duke Nukem, Doom, Final Fantasy, Dark Chronicles, Street fighter, marvel vs capcom, mortal kombat, Tekken, soul calibur, dragon ball, mass effect, the Witcher.
The first time I faced Sepiks Prime in Destiny, with that escalating music during the battle, I found it epic. Now, I no longer have those 'wow' moments in Destiny.
There's a whole bunch in Nier Automata where boss attacks and other environmental storytelling bits are timed to the music.
The boss android who "wants to be beautiful" for example launches projectiles in time to the music and the sound cues are in the correct key too.
Also there's that boss where you fight as 2B while 9S is off somewhere else trying to disable the power/security, and the exact moment that he kills the lights the music/vocals kicks in and the camera zooms right in. It's incredibly effective.
This is all Yoko Taro's homage to Ikaruga of course, which had very similar moments during boss battles and general gameplay which was timed to changes in the music.
Nier Automata's shifting soundtrack is another famous obvious one, with the same theme building and falling throughout areas and encounters.
Final Fantasy XV's Ifrit battle is forever ingrained in my memory because of how the OST ushered in new phases and even went seamlessly into the finishing cutscene.
Nikke does multi-phase OST stuff well too.
Also shout out to Atelier Sophie for this banger. I love the dichotomy of choir-like vocals over a metal song. I think this was for the Luard fight in the DLC, but it's been a minute.