Boss

(Note: this list does not include mini-bosses.)

The Legend of Zelda

 * Aquamentus
 * Dodongo
 * Manhandla
 * Gleeok
 * Digdogger
 * Gohma
 * Ganon

The Adventure of Link

 * Horsehead
 * Helmethead
 * Iron Knuckle
 * Carock
 * Gooma
 * Barba
 * Thunderbird
 * Dark Link

A Link to the Past

 * Ball and Chain Trooper
 * Armos Knights
 * Lanmolas
 * Moldorm
 * Agahnim
 * Helmasaur King
 * Arrghus
 * Mothula
 * Blind
 * Kholdstare
 * Vitreous
 * Trinexx
 * Ganon

Link's Awakening

 * Moldorm
 * Genie
 * Slime Eyes
 * Angler
 * Slime Eel
 * Facade
 * Evil Eagle
 * Hot Head
 * Nightmare
 * Giant Gel (shadow)
 * Agahnim (shadow)
 * Moldorm (shadow)
 * Ganon (shadow)
 * Lanmola (shadow)
 * Dethl (shadow)

Ocarina of Time

 * Queen Gohma
 * King Dodongo
 * Barinade
 * Phantom Ganon
 * Volvagia
 * Morpha
 * Bongo Bongo
 * Twinrova
 * Ganondorf
 * Ganon

Majora's Mask

 * Odolwa
 * Goht
 * Gyorg
 * Twinmold
 * Majora's Mask
 * Majora's Mask
 * Majora's Incarnation
 * Majora's Wrath

Oracle of Ages

 * Pumpkin Head
 * Head Thwomp
 * Shadow Hag
 * Eyesoar
 * Smog
 * Octogon
 * Plasmarine
 * Ramrock
 * Veran
 * Twinrova (secret)
 * Ganon (secret)

Oracle of Seasons

 * Aquamentus
 * Dodongo
 * Mothula
 * Gohma
 * Digdogger
 * Manhandla
 * Gleeok
 * Medelock
 * Onox
 * Twinrova (secret)
 * Ganon (secret)

Four Swords

 * Plant Nightmare
 * Ice Monster
 * Master Flame
 * Vaati

The Wind Waker

 * Gohma
 * Kalle Demos
 * Gohdan, the Great Arbiter
 * The Monsterous Helmaroc King
 * Jalhalla, Protector of the Seal
 * Molgera, Protector of the Seal
 * Puppet Ganon
 * Ganondorf

Four Swords Adventures

 * Helmaroc King
 * Jalhalla
 * Dodongo
 * Vaati
 * Ganon

The Minish Cap

 * Big Green ChuChu
 * Gleerok
 * Mazaal
 * Big Octorok
 * Gyorg Pair
 * Vaati
 * Vaati Reborn
 * Vaati Transfigured
 * Vaati's Wrath

Twilight Princess

 * Diababa
 * Fyrus
 * Morpheel
 * Stallord
 * Blizzeta
 * Armogohma
 * Argorok
 * Zant
 * Princess Zelda
 * Ganon
 * Ganondorf

Phantom Hourglass

 * Blaaz
 * Cyclok
 * Crayk
 * Diabolical Cubus Sisters
 * BangoRongo
 * Gleeok
 * Eox
 * Bellum
 * Phantom Ship
 * Linebeck