Oh wow this is gonna be tough for me. I'll try to keep it 20 total, I don't want to be here all day. While the top 3 are there for a reason, the rest are in no particular order.
LoZ:
Overworld Theme
AoL:
Palace Theme
ALttP:
Hyrule Castle
Dark World
Death Mountain
LA:
Ballad of the Wind Fish
OoT:
Lost Woods
Kakariko Village (past and future)
Guru Guru's Song
Gerudo Valley
Spirit Temple
Inside Ganon's Tower
MM:
Song of Healing
Clock Tower: First Day
Oath To Order
Deku Palace
Stone Tower
Majora's Incarnation
WW:
Outset Island
Ocean Theme
Dragon Roost Island
Gohdan
Molgera
Farewell Hyrule King
TP:
Midna's Lament
Lamentation of the Spirits
Horse Battle
King Bulbin
Blizzeta 2nd stage
Hidden Village
Ganondorf
MC:
Palace of Winds
ST:
Overworld (both)
Tower of Spirits
Linebeck's Theme
Facing the Demon Train
Final Battle: Protecting Princess Zelda
Final Battle: Malladus
SS: (oh crap...)
Ballad of the Goddess
Legend of Skyloft
Skyloft
Groose's Theme
Romance in the Air
Faron Woods
Stalfos (and Scervo's) Theme
Ghirahim's Themes (all of them)
Earth Temple
Pumpkin Pasttime
Lanayru Desert (present and past)
Lanayru Mining Facility (past and present)
Koloktos / Moldarach
Farore's Courage
Guardians Awaken
Lanayru Sand Sea
Sailing the Sand Sea
Inside the Sand Ship (past)
Din's Power
Fire Sanctuary
Dejected Groose
Levias battle
Bioclyte battle
Song of the Hero
Present at Peace
Dramatic Descent
Battlefield of Demise
Demise & Final Demise
Fi's Gratitude
Staff Roll
....Dadgummit, I tried so hard, but Zelda music is just too awesome!
3. Last Day (MM)
2. Past At Peace (SS)
1. Staff Credits / Opening Theme (WW)