1. The Legend of Zelda
The original is still my favorite but would I consider it the best? Probably not. I can accept both Ocarina of Time and A Link to the Past as objectively better games, but nostalgia is a powerful thing. There are, however, some things that the original still does better than any other Zelda.
First off is the second quest after you beat the game which is just brilliant. The overworld stays the same but they change the locations of the items, stores and dungeons. And speaking of dungeons, there's 9 completely new ones added to the second quest making it a total of 18 dungeons in this game. I can't remember any other Zelda game having that many.
Second is the lack of handholding and linearity. Here you had to find out what to do next on your own and you can beat the dungeons in any order (to some extent).
And third would be it's focus on gameplay rather than story. It completely lacks any sort of narrative which feels very refreshing to me. That doesn't mean that I dismiss the games that are heavier on the stories, but sometimes it can get a bit much.
2. Ocarina of Time
I prefer 2D over 3D but Ocarina of Time is just so good that I might actually consider it the "best". My favorite part are the dungeons. Especially the Forest-, Water- and Spirit (desert) temple. What sticks out to me is, although great, not the puzzles and design but the atmosphere and music. I rank the temples in Ocarina of Time as the best in the series. The same goes for the bosses. Gohma, Volvagia and Twinrova ranks as some of my favorites but Phantom Ganon has to be best of the bunch. I love the first part of the battle where he comes through the paintings.
The character design is really bad occasionally though. What were you thinking, Nintendo? *sigh*
2. A Link to the Past
I chose to put this in tied second with Ocarina because even if I could give a slight edge to either game, I feel like they bring the best from each style.
Gotta love the intro with the rain. What a way to start the game. Might just be the best intro ever. The game is just so memorable from beginning to end. Getting Zora's flippers, arriving in Dark World, the flute boy, reuniting the smiths (not the band!), it just goes on.
If there's one thing that holds the game back it is the dungeons. They're not bad but they're not very good either in my opinion. Tower of Hera, Skull Woods, Ice Palace, Misery Mire and Turtle Rock all suffer from various design flaws. Especially Skull Woods where you can completely skip portions. Thieves' Town is one of my all time favorites though, with a great twist at the end.
4. Zelda II: Adventure of Link
Love the gameplay. Very underrated. It would be awesome if they tried doing something like this again in the future.
Oh, and Thunderbird/Great Palace still gives me the feels every single time. And the Fokkas. How can you not love an enemy named Fokka?
5. Link's Awakening
Memorable characters. Especially Tarin. Seeing him turned into a raccoon or getting chased by bees always make me smile. Dungeons are a bit meh, but there's so much more to this game.
6. A Link Between Worlds
It's like a love letter to everyone who grew up with A Link to the Past. Not nearly as memorable but actually has better dungeons.
7. Breath of the Wild
Awesome overworld. Not so awesome dungeons. Or rather no dungeons at all, at least not in the classic sense. Also, all bosses are just the same design reused with some minor modifications. I love the game for what it is and does, but it just doesn't scratch that Zelda-itch for me.
8. Wind Waker
Beautiful artstyle. Might be the best looking game in the series. I have a love-hate relationship with the ocean. It was really exciting at first sailing around the ocean looking for treasure but it gets really tedious. So much that it deters me from playing the game.
9. Majora's Mask
Definitely the darkest game in the series. I love the atmosphere and the three day cycle. What really brings this game down is Tingle are the dungeons and bosses that doesn't compare at all to the ones in Ocarina. Another thing is that the game kinda feels like a hack since it uses a lot of art resources from Ocarina. A good hack, but a hack nonetheless.
10. Twilight Princess
Very bland. I'm just not feeling that Zelda-vibe from Twilight Princess. It had some nice ideas like using scents to track people as the wolf but overall, it stands as one of the weakest entries in the series.
*phew*