Hmmm.. this'll take me a while.
Final Fantasy in general:
FF4: Battles with the Four Fiends
FF5: Battle on the Big Bridge (Gilgamesh's Theme)
FF6: Zozo, Searching for Friends,
FF7: Electric de Chocobo, Those Who Fight Further (Boss Fight), J-E-N-O-V-A, Fiddle de Chocobo, Cait Sith's Theme
FF8: Force Your Way (boss fight), Premonition (I think this is vs Edea), The Man with the Machine Gun
FF9: Ukelele de Chocbo, Black Mage Village, Hunter's Chance, Jesters of the Moon, The Dark Messenger (vs Trance Kuja), Vamo'Alla Flamenco, You're Not Alone!, Tantalus's Theme, Sleepless City Treno, Amarant's Theme, Keeper of Time
FFX: Brass de Chocobo, Seymour's Ambition, Blitz Off!
Metal Gear Solid:
MGS: Boss Fight, Psycho Mantis' theme
MGS2: Peter's Theme, Yell "Dead Cell"
MGS3: Snake Eater
Katamari Damacy:
KD: Katamari on the Rocks, The Moon and the Prince, Fugue 7777, Que Sera Sera
WLK: DISCO PRINCE, Everlasting Love, Katamari on the Swing, Song for the King of Kings
Soul Calibur:
SC: Forever Onward, Apocalypse, Chasing Downstream
SC2: Ordinary Pain, Raise Thy Sword
Guilty Gear:
The Original (Faust's theme)
Haven't You Got Eyes in your Head (Slayer's theme)
Simple Life (Bridget's theme)
Writhe in Pain (Millia Rage's theme)
Pride and Glory (Kliff Undersn's theme)
Boom Town Blues (one of the story mode credits)
The Midnight Carnival (final battle in arcade)
Good Manners and Customs (Zappa's theme)
Liquor Bar and Drunkard (Johnny's theme)
Feel a Fear (Eddie's theme)
Meet Again (Justice's theme)
Vengeance is Mine (Kliff's #Reload theme)
The Vampire Saga (Slayer's #Reloard theme)
F-ZERO GX:
Beastman's theme
Super Arrow's theme
Falcon we Praise You (for pure cheesiness)
PJ's theme
Zoda's theme
Samurai Goroh's theme
Radiata Stories:
Paya Paya Song
Song of the Freedom Fighters (Warrior guild theme)
Magical World (Mage guild theme)
all of the Battle themes
Grand Battle Rush:
Buggy's finisher
Foxy's finisher
Ener's finisher
Shanks' finisher
Kirby:
Dedede's theme
wow…. that's a lot. and I know I forgot a lot..