Sub-Boss

A miniboss is a stronger than normal enemy that is located usually half-way through a dungeon, temple, or other locations. They are enemies which are harder to defeat and usually protect an item within a dungeon, such as equipment. An example would be the Stalfos in Ocarina of Time which one guards a small key, while another set guards the Fairy Bow. Some Minibosses are only defeated to proceed within the dungeon.

Link's Awakening

 * Rolling Bones
 * Hinox
 * Dodongo Snakes
 * Cueball
 * Master Stalfos
 * Gohma
 * Smasher
 * Grim Creeper
 * Fire Cephalopod
 * Blaino

Ocarina of Time

 * Deku Scrub Trio
 * Lizalfos
 * Big Octo
 * Stalfos
 * Poe Sisters
 * Flare Dancer
 * White Wolfos
 * Dark Link
 * Dead Hand
 * Iron Knuckle
 * Dinolfos

Majora's Mask

 * Dinofols
 * Gekko and Snapper
 * Wizzrobe
 * Gerudo Pirate
 * Wart
 * Gekko and Mad Jelly
 * Captain Keeta
 * Iron Knuckle
 * Igos du Ikana Servants
 * King Igos du Ikana
 * Garo Master
 * Gomess
 * Poe Sisters

Oracle of Ages

 * Giant Ghini
 * Swoop
 * Subterror
 * Armos Warrior
 * Smasher
 * Vire
 * Angler Fish
 * Blue Stalfos

Oracle of Seasons

 * Goriya Bros.
 * Facade
 * Calamareye
 * Agahnim
 * Syger
 * Vire
 * Poe Sisters
 * Frypolar

The Wind Waker

 * Bokoblin
 * Moblins
 * Mothula
 * Phantom Ganon
 * Darknut
 * Stalfos
 * Wizzrobe
 * Mighty Darknut
 * Cyclos
 * Big Octo

Four Sword Adventures

 * Chief Soldier
 * Shadow Link
 * Manhandla
 * Helmaroc King
 * Big Dark Stalfos
 * Phantom Ganon
 * Mace Knights
 * Big Dodongo

The Minish Cap

 * Madderpillar
 * Spiny ChuChu
 * Darknut
 * Big Blue Chuchu
 * Red Darknut
 * Black Knight

Twilight Princess

 * Ook (and Baba Serpents)
 * Dangoro
 * Shadow Kargaroc Rider
 * Twilit Bloat
 * Deku Toad (and Toados)
 * Skull Kid (and Puppets)
 * Death Sword
 * Darkhammer
 * Darknut
 * Aeralfos
 * Phantom Zant
 * King Bulblin

Phantom Hourglass

 * Giant Eye Plant
 * Eyefish
 * Jolene
 * Ghost Ship

Spirit Tracks

 * Mothula
 * Ice Keese
 * Snapper
 * Heatoise
 * Rocktite
 * Geozard Chief