Seeing how I finally got around to playing OoT recently.. well.. a week ago, when I got it with my Wii points card, I'll definitely mention at least one of the melodies that's gotten stuck in my head.
Saria's Song
Zelda's Lullaby
Song of Storms
As for KH songs..
Dierge of the Fourteenth
Xion's Theme
Lord of the Castle
The Graceful Assassin
Scythe of Petals (Marluxia has some also songs btw.. the other two are probably the best two final boss themes in the series.)
Deep Dive
The music to the BBS trailer in Final Mix+
The final boss theme of KH1 (World of Chaos)
End of the World
Fight to the Death
Darkness of the Unknown
Organization XIII Battle
Organization XIII Dilemma
Sacred Moon (TWTNW's theme)
Not KH or Zelda
The first world of R&CF: Tools of Destruction
The final world of previous said game (Damn.. I'm pretty annoyed that I have seemed to forgot its name.)
The chase music in NFS: Most Wanted
Unreal Tournament 3's menu music
Biohazard's (UT3) music
TimeSplitters
Siberia (TimeSplitters 2)
Space Station (TS2)
Chicago (TS2)
Mexican Mission (TS2/ FP)
Wild West (TS2)
Training Ground (TS2)
Mansion of Madness (TS: Future Perfect)
Scotland the Brave (TS: FP)
Ice Station (TS2)
Like a Monkey (TS: FP)
Subway (TS: FP)
I can't be arsed to add the links, but if I get the time, I guess I could.