Character Hacks:
Dark Link
MM Link and FD Link
MM3D Link
OoT3D Link
Gerudo Warrior
TP Link
Hero of Light

Story Hacks:
Zelda's Birthday 2008
Zelda's Eternal Youth 2015
Voyager of Time 2013
Nightmare 2008

Map Hacks:
Custom Dungeon by JeDDyDee 2013
Project Beta Triforce 2013-2016
Project Izou 2014
Hero of Hyrule 2014
Four Swords Arena Edition 2016

Beta Restoration Hacks:
Beta of Time
Zelda64 Recreation

Misc. Hacks:
Petrie's Challenge
Ocarina of Time Randomizer
Beta Quest 2015

(Note: Just like the GoldenEye and Perfect Dark sections, each type of hack will have its own banner down the line. WIP)