Gah, too many to list!
1. Super Mario Bros. theme
2. Legend of Zelda main theme
3. LoZ: OoT - Gerudo Vally
4. LoZ: OoT - Song of Storms
5. MGS2 main theme
Honorable mentions:
LoZ: OoT - Title screen music
LoZ: OoT - Fairy Fountain/game select screen
LoZ: OoT - Bolero of Fire
LoZ: OoT - Song of Time
LoZ: OoT - Shop music
LoZ: OoT - Sun's Song
LoZ: OoT - Kakariko Village
LoZ: OoT - Zora's Domain
LoZ: MM - Clock Town
LoZ: TP - Lake Hylia
LoZ: WW - Sailing theme
SM64 - Caste Theme
Kirby's Adventure - Rainbow Resort lvl 6
Kirby's Adventure - Yogurt Yard Forest
Kirby's Adventure - Vegetable Valley
And every other OoT song I'm forgetting...