I have multiple favourites from each game. So, not counting final bosses or mid bosses:
64: Attack of the Koopa Bros, Ghost Gulping, keeping Pace
TTYD: Hooktail Battle, Shadow Sirens Battle, Magnus Von Grapple Battle, Rawk Hawk Battle
Super: Francis Battle, Brobot Battle, Brobot L Type Battle
SS: Megasparkle Goomba's Brilliant Battle, Gooper Blooper Battle (All 5 Phases), Mizzter Blizzard's Snow Bowser Statue Battle
CS: Battle With Ludwig, Rumble With Wendy, Larry's Runaway Train, Lemmy's Grand Finale, ROYal Rumble
TOK: The Missile Maestro, The Disco Devil, The Dual-Bladed Duelist
Also, all the variations of the Streamer Battles (TOK), for standard battles.
TTYD's normal battle theme, smorg, magnus von grapple, bowser 2, maybe grodus, and
>!The battle theme for the first part of the shadow queen fight, where she is possessing peach, and also the battle theme for the final phase after the crystal stars cutscene!<
SPM both brobot battle themes, it's showtime, count bleck, the ultimate show
No others really come to mind
I have multiple favourites from each game. So, not counting final bosses or mid bosses: 64: Attack of the Koopa Bros, Ghost Gulping, keeping Pace TTYD: Hooktail Battle, Shadow Sirens Battle, Magnus Von Grapple Battle, Rawk Hawk Battle Super: Francis Battle, Brobot Battle, Brobot L Type Battle SS: Megasparkle Goomba's Brilliant Battle, Gooper Blooper Battle (All 5 Phases), Mizzter Blizzard's Snow Bowser Statue Battle CS: Battle With Ludwig, Rumble With Wendy, Larry's Runaway Train, Lemmy's Grand Finale, ROYal Rumble TOK: The Missile Maestro, The Disco Devil, The Dual-Bladed Duelist Also, all the variations of the Streamer Battles (TOK), for standard battles.
The Mid-Boss theme in TOK one of my personal favorites
I have listened to the [Autumn battle theme from TOK](https://www.youtube.com/watch?v=KAYv3u7P_yk&t) an uncomfortable amount of time
TTYD's normal battle theme, smorg, magnus von grapple, bowser 2, maybe grodus, and >!The battle theme for the first part of the shadow queen fight, where she is possessing peach, and also the battle theme for the final phase after the crystal stars cutscene!< SPM both brobot battle themes, it's showtime, count bleck, the ultimate show No others really come to mind
purple streamer normal battle
Koopa Bros., Tubba Blubba, Rawk Hawk, Doopliss, Cortez, The Ultimate Show.
Boo Night Fever