Mario Series
SMB2 ------- Underground Theme
SMW -------- Forest of Illusion
SMW2YI --- Map Theme
SMRPG ---- Super Pipe House
SM64 -------- Dire Dire Docks, Metal Cap Mario, Flying Cap Mario, Hazy Maze Cave, Bob-omb Battlefield, Castle Interior
MK64 -------- Koopa Troopa Beach, Frappe Snowland, Toad's Turnpike, Rainbow Road
SSB ---------- After you beat Master Hand, while the score comes up.
SMS --------- Delfino Plaza, Outside Hotel Delfino, Noki Bay Underwater, SAND BIRD!
SSBM ------- Mute City
M&LSS------ the Seaside song...
Sonic series
StH ----------- Special Area, Invincibility, Act Complete
StH2 --------- Emerald Hill Zone, Chemical Plant Zone
StH3 --------- Angel Island Zone, Hydrocity Zone
S&K ---------- Mushroom Hill Zone
Banjo Series
BK ------------ Treasure Trove Cove, Gruntilda's Lair Click Clock Wood version
BT ------------- Jiggy Wiggy's Temple, Grunty's Industry Interior
Other
StarFox64 ---------- Title Screen, Corneria, Katina, Mission Accomplished, Zoness, Ending
Bomberman 64 --- Opening, Green Garden, Red Mountain, White Glacier, Black Fortress, Rainbow Palace, Boss Battle, Altair Battle, Sirius Battle, Level Complete, Ending
And yeah, most stuff by Yasunori Mitsuda.