As you say Metacritic is ballz and doesn't even have scores for some Zelda games; so I dragged this out of GameRankings and got rid of remakes and collections for you to use if you want.

1		N64	The Legend of Zelda: Ocarina of Time Nintendo, 1998	97.54% 28 Reviews
2		WII	The Legend of Zelda: Twilight Princess Nintendo, 2006	94.58% 84 Reviews
3		GC	The Legend of Zelda: The Wind Waker Nintendo, 2003	94.43% 94 Reviews
4		WII	The Legend of Zelda: Skyward Sword Nintendo, 2011	93.15% 61 Reviews
5		SNES	The Legend of Zelda: A Link to the Past Nintendo, 1992	92.87% 15 Reviews
6		GBC	The Legend of Zelda: Oracle of Ages Flagship/Nintendo, 2001	92.20% 20 Reviews
7		N64	The Legend of Zelda: Majora's Mask Nintendo, 2000	91.95% 33 Reviews
8		GBA	The Legend of Zelda: A Link to the Past Nintendo, 2002	91.74% 39 Reviews
9		GBC	The Legend of Zelda: Oracle of Seasons Flagship/Nintendo, 2001	91.37% 23 Reviews
10		3DS	The Legend of Zelda: A Link Between Worlds Nintendo, 2013	90.55% 55 Reviews
11		GBA	The Legend of Zelda: The Minish Cap Flagship/Nintendo, 2005	90.36% 67 Reviews
12		GB	The Legend of Zelda: Link's Awakening Nintendo, 1993	89.82% 8 Reviews
13		DS	The Legend of Zelda: Phantom Hourglass Nintendo, 2007	88.82% 75 Reviews
14		DS	The Legend of Zelda: Spirit Tracks Nintendo, 2009	87.05% 55 Reviews
15		GC	The Legend of Zelda: Four Swords Adventures Nintendo, 2004	84.51% 61 Reviews

I still think OoT is higher than it should be, but overall, its just a matter of which amazing game is more amazing.

I hope there's no one that seriously believes OoT is STILL the best Zelda game ever. Because that would be a big insult to all future Zelda games.

Same with people that claim Super Mario 64 is the best 3D Mario platformer. You're telling me Nintendo's first 3D game also happens to be their best one? Lol. (not directed at you). 

Thanks. Tables made it easier to read. I removed the box-arts though.

OT: I would imagine Link To The Past a bit higher, and Majora's Mask. Also, hoare the "Oracles'" so far apart?

Phantom Hourglass was only Zelda game I played that I really disliked, so of those would deifnitely rank it the lowest.

Minish Cap would actually be near the top with a Link to the Past.

Minish Cap isn't higher, this list breaks my heart. Gamerankings is a bit better.

Worst: Windwaker, I'm not a fan of the art style at all.

Best: The minish cap, the only zelda i remember playing for a long time...during class...in high school..on an emulator.

The Faces of Evil...

The worst 3D Zelda game is Twilight Princess, but overall the worst Zelda game has to be Zelda 2!

Four Sword Adventures is one of the best games I've played in my life; that is, if you play it properly: four GBAs connected to the GC, with friends :D