I'll focus on the lesser-known ones:
Million Knights Vermilion - Bloody Nightmare
Million Knights Vermilion - Archenemy
Warsong (Langrisser) - Player Phase 1 (Friendly Fight)
Choujin Sentai Jetman - Area A
Choujin Sentai Jetman - Last Area
Captain Tsubasa II: Super Striker - Kojiro Hyuga's Theme (Toho Team)
Captain Tsubasa II: Super Striker - Tsubasa's Cyclone Shoot Theme
Touhou: Embodiment of Scarlet Devil - Cirno's Theme
Plasma Sword: Nightmare of Bilstein - Illusion of Peace
Castlevania Judgment - An Empty Tome (Shanoa's Theme)
King of Fighters 99 - KD-0079 (Heroes Team Theme)
King of Fighters 97 - Rhythmic Hallucination
King of Fighters: Maximum Impact - Enigma Machine (Iron Hell Stage)
Xenosaga Episode I: Der Wille zur Macht - Battle Theme
Chip 'n Dale: Rescue Rangers - Zone J
EDIT: I can't believe I forgot about Bucky O'Hare... It deserves a mention. Here and here. Done.
NSFW:
Bible Black: La Noche de Walpurgis - Bible Black
Bible Black: La Noche de Walpurgis - Grimoire
