This will take me a while so, I'll just post this as a reminder.

• Story/Plot:
  1st) Twilight Princess
  2nd) Majora's Mask
  3rd) Minish Cap
  
  
• Main Characters:
  1st) Oracle of Ages/Seaons
  2nd) Ocarina of Time
  3rd) Twilight Princess
  
  
• Minor Charaters:
  1st) Wind Waker
  2nd) Majora's Mask
  3rd) Minish Cap
  
  
• Writing:
  1st) Twilight Princess
  2nd) Skyward Sword
  3rd) A Link Between Worlds
  
  
• Overworld:
  1st) A Link to the Past
  2nd) A Link Between Worlds
  3rd) Minish Cap
  
  
• Side Quests:
  1st) Skyward Sword
  2nd) Ocarina of Time
  3rd) A Link Between Worlds
  
  
• Collecting:
  1st) Oracle of Ages/Seasons
  2nd) Wind Waker
  3rd) Ocarina of Time
  
  
• Gimmicks/Innovations:
  1st) A Link Between Worlds
  2nd) Ocarina of Time
  3rd) Majora's Mask
  
  
• Dungeons:
  1st) Majora's Mask
  2nd) Skyward Sword
  3rd) A Link to the Past
  
  
• Controls:
  1st) A Link Between Worlds
  2nd) A Link to the Past
  3rd) Skyward Sword
  
  
• Combat:
  1st) Wind Waker
  2nd) Skyward Sword
  3rd) Majora's Mask
  
  
• Exploration:
  1st) A Link to the Past
  2nd) A Link Between Worlds
  3rd) Wind Waker
  
  
• Puzzles:
  1st) Majora's Mask
  2nd) Oracle of Ages/Seasons
  3rd) Skyward Sword
  
  
• Items:
  1st) Wind Waker
  2nd) Skyward Sword
  3rd) A Link to the Past
  
  
• Bosses:
  1st) Majora's Mask
  2nd) Skyward Sword
  3rd) Link's Awakening
  
  
• Graphics:
  1st) Minish Cap
  2nd) Wind Waker
  3rd) A Link Between Worlds
  
  
• Art Style:
  1st) Minish Cap
  2nd) A Link Between Worlds
  3rd) Twilight Princess
  
  
• Music:
  1st) A Link Between Worlds
  2nd) Ocarina of Time
  3rd) Twilight Princess
  
  
• Tone:
  1st) Majora's Mask
  2nd) Twilight Princess
  3rd) Wind Waker
  
  
• Best Zelda Ever:
  1st) A Link to the Past
  2nd) A Link Between Worlds
  3rd) Skyward Sword

Story
1. The Legend of Zelda: Ocarina of Time
2. The Legend of Zelda (NES)
3. The Legend of Zelda: Majora's Mask

Main Characters
1. The Legend of Zelda: Ocarina of Time
2. The Legend of Zelda: Twilight Princess
3. The Legend of Zelda; The Wind Waker

Minor Characters
N/A

Writing
1. The Legend of Zelda (NES)
2. The Legend of Zelda: Ocarina of Time
3. The Legend of Zelda: The Wind Waker

Overworld
1. The Legend of Zelda (NES)
2. The Legend of Zelda: Ocarina of Time
3. The Legend of Zelda: A Link To The Past

Side Quests
N/A

Collecting
N/A

Innovations
1. The Legend of Zelda (NES)
2. The Legend of Zelda: Ocarina of Time
3. The Legend of Zelda: Ocarina of Time (Z-Targeting)

Dungeons
1. The Legend of Zelda: A Link to the Past
2. The Legend of Zelda: Twilight Princess
3. The Legend of Zelda: The Wind Waker

Controls
1. The Legend of Zelda (NES)
2. The Legend of Zelda: The Wind Waker
3. The Legend of Zelda: Ocarina of Time

Combat
1. 1. The Legend of Zelda: A Link to the Past
2. The Legend of Zelda (NES)
3. The Legend of Zelda: The Wind Waker

Exploration
1. The Legend of Zelda (NES)
2. The Legend of Zelda: Ocarina of Time
3. The Legend of Zelda: A Link to the Past

Puzzles
NO FUCK THIS

Items
1. The Legend of Zelda: Ocarina of Time
2. The Legend of Zelda (NES)
3. The Legend of Zelda: The Wind Waker

Bosses
N/A

Graphics
1. The Legend of Zelda: The Wind Waker
2. The Legend of Zelda: A Link to the Past
3. The Legend of Zelda: Twilight Princess 

ArtStyle
1. The Legend of Zelda: The Wind Waker
2. The Legend of Zelda: A Link to the Past
3. The Legend of Zelda: Twilight Princess 

Music
1. The Legend of Zelda (NES)
2. The Legend of Zelda: The Wind Waker
3. The Legend of Zelda: A Link to the Past

Tone
1. The Legend of Zelda: Ocarina of Time
2. The Legend of Zelda: (NES)
3. The Legend of Zelda: A Link to the Past

Best Zelda
1. The Legend of Zelda (NES)
2. The Legend of Zelda: Ocarina of Time
3. The Legend of Zelda: The Wind Waker

Tagged for later when I get home.

Story/Plot
1. Skyward Sword
2. Ocarina of Time
3. Twilight Princess

Main Characters
1. Skyward Sword
2. Ocarina of Time
3. Twilight Princess

Minor Characters
1. Skyward Sword
2. Ocarina of Time
3. A Link Between Worlds

Writing
1. Skyward Sword
2. Ocarina of Time
3. Twilight Princess

Overworld
1. Ocarina of Time
2. A Link Between Worlds
3. Skyward Sword (I'm considering Faron Woods, Eldin Volcano, and Lanaryu Desert the "overworld")

Side Quests (Which games had the best non-story content)
1. Skyward Sword
2. Ocarina of Time
3. A Link Between Worlds

Collecting
1. A Link Between Worlds
2. Skyward Sword
3. Ocarina of Time

Gimmicks/Innovations
1. Ocarina of Time
2. Skyward Sword
3. A Link Between Worlds

Dungeons
1. Ocarina of Time
2. Skyward Sword
3. Twilight Princess

Controls
1. Twilight Princess
2. Ocarina of Time
3. Skyward Sword

Combat
1. Skyward Sword
2. Twilight Princess
3. Ocarina of Time

Exploration
1. Ocarina of Time
2. Skyward Sword
3. A Link Between Worlds

Puzzles
1. A Link Between Worlds
2. Skyward Sword
3. Twilight Princess

Items
1. A Link Between Worlds
2. Skyward Sword
3. Twilight Princess

Bosses
1. Twilight Princess
2. Ocarina of Time
3. Skyward Sword

Graphics
1. Skyward Sword
2. The Wind Waker HD (if not counting remakes as separate, then Twilight Princess)
3. Ocarina of Time 3D (if not counting remakes as separate, then The Wind Waker)

Art Style
1. Ocarina of Time
2. Skyward Sword
3. Twilight Princess

Music
1. Ocarina of Time
2. Twilight Princess
3. Skyward Sword

Tone
1. Twilight Princess
2. The Wind Waker
3. Ocarina of Time

Best Zelda Ever
1. Ocarina of Time
2. Twilight Princess
3. Skyward Sword

Gotta tag this!

It's great to see so many people interested! Feel free to take your time with these... January 1 is the soonest possible deadline, not an absolute. If people keep on voting or changing, I'm willing to give another week or two to do so.

Story
1. The Legend of Zelda: Ocarina of Time
2. The Legend of Zelda: Wind Waker
3. The Legend of Zelda: Majora's Mask

Main Characters

1. The Legend of Zelda: Ocarina of Time
2. The Legend of Zelda: The Wind Waker
3. The Legend of Zelda: Skyward Sword

Minor Characters
1. The Legend of Zelda: Majora's Mask
2. The Legend of Zelda: Link's Awakening DX
3. The Legend of Zelda: Spirit Tracks

Writing
1. The Legend of Zelda: Ocarina of Time
2. The Legend of Zelda: The Wind Waker
3. The Legend of Zelda: A Link to the Past

Overworld
1. The Legend of Zelda: Twilight Princess
2. The Legend of Zelda NES
3. The Legend of Zelda: A Link to the Past

Side Quests
1. The Legend of Zelda: Majora's Mask
2. The Legend of Zelda: Link's Awakening DX
3. The Legend of Zelda: Ocarina of Time


Collecting
1. The Legend of Zelda: Majora's Mask
2. The Legend of Zelda: Spirit Tracks
3. The Legend of Zelda: Minish Cap

Innovations
1. The Legend of Zelda: Ocarina of Time
2. The Legend of Zelda: A Link to the Past
3. The Legend of Zelda: Skyward Sword


Dungeons
1. The Legend of Zelda: Oracle of Ages
2. The Legend of Zelda: Wind Waker
3. The Legend of Zelda: Ocarina of Time

Controls
1. The Legend of Zelda: The Wind Waker
2. The Legend of Zelda: Phantom Hourglass/Spírit Tracks
3. The Legend of Zelda: Skyward Sword

Combat
1. 1. The Legend of Zelda: The Wind Waker
2. The Legend of Zelda: Skyward Sword
3. The Legend of Zelda: Ocarina of Time

Exploration
1. The Legend of Zelda NES
2. Zelda II The Adventure of Link
3. The Legend of Zelda: A Link Between Worlds

Puzzles
1. The Legend of Zelda: Oracle of Ages
2. The Legend of Zelda: Link's Awakening DX
3. The Legend of Zelda: Spirit Tracks

Items
1. The Legend of Zelda: Majora's Mask (Masks count, right?)
2. The Legend of Zelda: A Link to the Past
3. The Legend of Zelda: Ocarina of Time

Bosses
1. The Legend of Zelda: Spirit Tracks
2. The Legend of Zelda: Oracle of Ages
3. The Legend of Zelda: Ocarina of Time

Graphics
1. The Legend of Zelda: The Wind Waker
2. The Legend of Zelda: Skyward Sword
3. The Legend of Zelda: Twilight Princess

ArtStyle
1. The Legend of Zelda: Majora's Mask
2. The Legend of Zelda: Twilight Princess
3. The Legend of Zelda: Wind Waker

Music
1. The Legend of Zelda: Ocarina of Time
2. The Legend of Zelda: Link's Awakening (ballad of windfish, tal tal heighs)
3. The Legend of Zelda: Wind Waker/Spirit Tracks

Tone
1. The Legend of Zelda: Majora's Mask
2. The Legend of Zelda: Wind Waker
3. The Legend of Zelda: Ocarina of Time

Best Zelda
1. The Legend of Zelda: Majora's Mask
2. The Legend of Zelda: Wind Waker
3. The Legend of Zelda: Ocarina of Time

I didn't end Skyward Sword, the NES's zeldas and the four swords. I didn't even started A link between worlds. All the others I finished.

Story
1.Skyward Sword
2.Majoras Mask
3.Wind Waker

Main Characters
1.Majoras Mask
2.Twilight Princess
3.Ocarina of Time

Minor Characters
1.Majoras Mask
2.Skyward Sword
3.Links Awakening

Writing
1.Skyward Sword
2.Twilight Princess
3.Wind Waker

Overworld
1.Twilight Princess
2.Ocarina of Time
3.Wind Waker

Side Quests
1.Ocarina Of Time
2.Majoras Mask
3.Skyward Sword

Collecting
1.Majoras Mask
2.Twilight Princess
3.Skyward Sword

Innovations
1.Ocarina of Time
2.Skyward Sword
3.A link to the Past

Dungeons
1.Twilight Princess
2.Ocarina of Time
3.Skyward Sword

Controls
1.Skyward Sword
2.Ocarina of Time
3.Wind Waker

Combat
1.Ocarina Of Time
2.Wind Waker
3.Skyward Sword

Exploration
1.Wind Waker
2.Majoras Mask
3.Ocarina of Time

Puzzles
1.Twilight Princess
2.Skyward Sword
3.Wind Waker

Items
1.Skyward Sword
2.Ocarina of Time
3.Links Awakening

Bosses
1.Twilight Princess
2.Skyward Sword
3.Ocarina of Time

Graphics
1.Skyward Sword
2.Twilight Princess
3.Wind Waker

ArtStyle
1.Twilight Princess
2.Ocarina of Time
3.Majoras Mask

Music
1.Ocarina of Time
2.A link to the past
3.Wind Waker

Tone
1.Majoras Mask
2.Twilight Princess
3.Skyward Sword

Best Zelda
1.Ocarina of Time
2.Skyward Sword
3.Twilight Princess

Story/Plot (Pretty Basic)

1 - OOT
2 - Majoras mask
3 - A Link Between Worlds

Main Characters (aka which Zelda had the best Link, Zelda, and main antangonist)

1 - Ocarina Of Time
2 - Twilight Princess
3 - Majoras Mask

Minor Charaters (which had the best one-shot characters, like Linebeck, the Old Man, TIngle, the Great Deku tree, Ravio, etc.)

1 - Majoras Mask
2 - Ocarina Of Time/Windwaker tied
3 - A Link Between worlds (I'm noticing a pattern)

Writing (Which story was told the most elegantly? AKA the award Zelda 2 likely won't win.)

1 - Ocarina Of Time
2 - Twilight Princess
3 - A Link Between Worlds

Overworld (Which was the best designed, had the most stuff to do, was the most fun to travel around, etc.)

1 - A Link to the Past
2 - a Link Between Worlds
3 - Ocarina Of Time

Side Quests (Which games had the best non-story content)

1 - MajorasMask
2 - Ocarina Of Time
3 - Twilight Princess

Collecting (Which games had the best "collect every heart piece/upgraded item/little octopus things" factor?)

1 - A Link Between Worlds
2 - A Link to the Past
3 - Ocarina of Time/Majoras Mask

Gimmicks/Innovations (Which game introduced the most great ideas, be it parallel worlds, Z-targetting, motion controls, etc.)

1 - Link to the Past (PArallel worlds mechanic is one reused for the decades)
2 - Ocarina of Time (Z-targetting)
3 - Twilight Princess (Motion controls without turning the game into a minigame haven)

Dungeons (Which game had the best collection of these? Overall consistency beats one-hit wonders here.)

1 - Ocarina Of time
2 - A Link to the Past
3 - Twilight Princess

Controls (Do you prefer the conventional D-Pad and buttons of old, Wind Waker's dual analogs, Skyward's motion controls, etc.)

1 - A link between worlds
2 - A Link to the past
3 - Wind Waker

Combat (In which game was it the funnest to fight enemies other than bosses?)

1 - Ocarina of time
2 - Wind Waker
3 - A Link Between Worlds

Exploration (Which game made it the most fun to become intimate with every square inch of the game's world?)

1 - Zelda 1
2 - A Link to the Past
3 - A Link Between Worlds

Puzzles (Which game had the most ingeniously designed and clever Puzzles?)

1 - MajorasMask/Ocarina of time tied
2 - Wind Waker
3 - A Link Between Worlds

Items (Which game has the best collection of these and uses them the most effectively?)

1 - A Link to the Past
2 - A Link Between Worlds
3 - Ocarina of time/windwaker

Bosses (Which are the most epic, best-designed, and are simply the most genious?)

1 - Ocarina of time
2 - Twilight Princess
3 - A Link Between Worlds

Graphics (Which game is the best-looking Zelda from a more technical standpoint? Try also focusing on things like distinct sprites that stand out from the background, the little death effects of enemies, etc., rather than just resolution, polygon count, and textures.)

1 - Ocarina of time 3d
2 - Twilight Princess
3 - A Link between worlds

Art Style (Do you prefer Wind Waker's Cartoon vibe, Twilight Princesss darker shades, Skyward Sword's mix of color and realism, etc.)

1 - Ocarina of time
2 - Majoras Mask
3 - Twilight Princess

Music (aka Soundtrack)

1 - Ocarina of time
2 - Windwaker
3 - A Link Between Worlds

Tone (Which game most effectively sets the tone it tries to make for itself? Examples may include the desolation of the original game, the silly humor of Link's Awakening, the impending doom of Majora's Mask, etc.)

1 - Majoras Mask
2 - Ocarina of Time
3 - Twilight Princess

Best Zelda Ever (Duh!)

1 - Ocarina of time
2 - Majoras Mask
3 - A Link Between Worlds/Twilight princess