By series
Mario Series
SMB: Overworld, Underwater, Underground (classics)
SMW: Overworld, Forest of Illusions map
SMK: Donut Plains
YI: Title Screen (Same song was used for Yoshi's Island in M&L:PiT)
SM64: Dire Dire Rocks, Bowser's fight song, Bowser Courses
PM:TTYD: Glitz Pit, Rawk Hawk's battle song
MKDS: Waluigi Pinball
M&L:SS: Ocean and beaches
Zelda Series
LoZ: Overworld, credits
AoL: Temple
LttP: Hyrule Castle, Zelda's theme (AKA Zelda's Lullaby), Dark Overworld, Dark World Death Mountain, Credits
LA: Ballad of the Windfish, Tal Tal Heights
OoT: Saria's Song, Song of Storms, Nocturne of Shadow, Gerudo Valley, Epona's Song, Ganondorf battle, Credits
MM: New Wave Bossa Nova, Stone Temple
TWW: Dragonroost Island, Farewell Hyrule King, Credits
TMC: Clouds, Credits, Game Over, Dungeon in the sky (can't remember the name of it)
Super Smash Bros. series
SSB: Credits, Hyrule Castle, Sector Z, The Mushroom Kingdom
SSBM: Opening, Menu 2, Target Test, Pokemon Battle 1 and 2, SMB3 (alternate tune for Yoshi's Island stage), Temple, Icicle Mountain, Rainbow Cruise
Pokemon series
R/B/Y: Gym Leader Battle, Trainer Battle, Pallet Town, Saffron City, Inside Gym, Surfing
G/S/C: Most of the Battle themes, Burned Tower,
R/S/E: Dive
Colosseum: Pyrite, most of the Battle themes, The Under, Credits, Relic Stone
XD: Gale of Darkness: SS Libra, ONBS building.
Mystery Dungeon: Mt. Freeze and more
Other
MP: Magmoor Caverns
That's all I'm gonna list for now.