Sub-Boss

A Mini-boss, also known as a Middle Boss, is generally one particular enemy or a group of common enemies which are harder to defeat

Characteristics
Mimi-bosses usually protect an item within a dungeon or other locations. Most of the time, they must be defeated to proceed within a dungeon or area. A common characteristic that distinguishes a mini-boss from a regular enemy is a particular battle theme played during the encounter, which is different from the usual enemy theme. They may return later as common enemies, likely because Link will have new tools and weapons to defeat them more easily. They may come in groups, as in the case of common enemies. If they are in a room, the door usually locks until they are defeated.

The Legend of Zelda

 * Almost every boss is eventually fought again as minibosses, as they no longer guard Heart Containers or Triforce fragments in their later appearances.
 * Blue Gohma
 * Patra

The Adventure of Link

 * Rebonack returns as a mini-boss in the Three-Eye Rock Palace.
 * Mazura appears a second time as the mini-boss of the Palace on the Sea in the Japanese version of the game. An Iron Knuckle takes its place in the international versions.

A Link to the Past

 * Ball and Chain Trooper
 * The first three bosses of the game (Armos Statues, Lanmolas and Moldorm) return in Ganon's Tower as mini-bosses.
 * In the Palace of the Four Sword (exclusive to the Game Boy Advance version), the first four bosses from the Dark World dungeons (Helmasaur King, Arrghus, Mothula and Blind the Thief) return as stronger mini-bosses.

Link's Awakening

 * Rolling Bones
 * Hinox
 * Dodongo Snakes
 * Cue Ball
 * Master Stalfos
 * Gohma
 * Smasher
 * Grim Creeper
 * Blaino

Ocarina of Time

 * Lizalfos
 * Big Octo
 * Stalfos
 * Meg
 * Flare Dancer
 * White Wolfos
 * Dark Link
 * Dead Hand
 * Iron Knuckle

Majora's Mask

 * Dinofols
 * Gekko (who fights Link along with a Snapper in Woodfall Temple, and along with samples of Mad Jelly in Great Bay Temple).
 * Wizzrobe (icy variation in Snowhead Temple, fiery variation in Ancient Castle of Ikana).
 * Gerudo Pirate
 * Wart
 * Captain Keeta
 * Iron Knuckle
 * Big Poe
 * Igos du Ikana Servants
 * King Igos du Ikana
 * Garo Master
 * Gomess

Oracle of Ages

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

Oracle of Seasons

 * Brother Goriyas
 * Facade
 * Omuai
 * Agunima
 * 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
 * Dodongos
 * Big Dark Stalfos
 * Gohma
 * Ball and Chain Soldiers
 * Big Dodongo

The Minish Cap

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

Twilight Princess

 * Ook
 * King Bulblin & Lord Bullbo
 * Dangoro
 * Twilit Carrier Kargarok
 * Twilit Bloat
 * Deku Toad
 * Skull Kid & Puppets
 * Death Sword
 * Darkhammer
 * Darknut
 * Aeralfos
 * Phantom Zant

Phantom Hourglass

 * Giant Eye Plant
 * Massive Eye
 * Jolene
 * Phantom x9

Spirit Tracks

 * Mothula
 * Rocktite
 * Geozard Chief
 * Big Blin
 * Snapper
 * Heatoise
 * Stalfos Warrior
 * Dark Link

Skyward Sword

 * Stalfos
 * Lizalfos
 * Stalmaster
 * Moldarach (second fight)
 * Scervo
 * Magmanos
 * Dark Lizalfos
 * Moldorm
 * Metal Shield Moblin
 * Dreadfuse

A Link Between Worlds

 * Armos
 * Stalfos
 * Heedles
 * Goriyas
 * Gigabari
 * Gibdos & Mini-Moldorms
 * Eyegores
 * Devalants
 * Big Pengator & Pengators
 * Fire Gimos
 * Moldorm
 * Gigabari
 * Fire Ball and Chain Soldier
 * Arrghus