I haven't even played my copy of Skyward Sword but i can safely is it's 1 million times greater than the brown dreary & drenched barren OOT wanna'biein' Twilight Princess . I've only played 15 minutes of TP, so take my bogus Bull dookie with an enormous grain of salt.
For now, I'll just pick Link's Awakening and call it a day, followed by the original.

I know ALTTTP will be my favorite 2D Zelda, with Skyward Sword being my favorite 3D, it's just destiny baby.

My favorite is The Legend of Zelda: How Many "Favorite Zelda" Threads Can There Be On NL.

Hahaha! Oh you.

A Link to the Past is the best Zelda game. If you want to know why go read the May issue of Nintendo Power.

Wind Waker. Creative, the story is amazing, I love the new characters and the idea of the ocean. Some of my favorite Zelda quotes are from this game. I think the graphics are unique and even though people say it's kiddish, I couldn't see wind waker with any other graphics honestly. The story had some dark parts in it. It was the first Zelda game I played, so I have a personal connection to it. I love the music. Every single track is beautiful and different. My favorite from that game is Molgera! So catchy! Would love to see this art style on the wii, don't hate on me, I just love wind waker. It needs a lot more credit than it gets.

I love Wind Waker's awesome style. I just wish it had more dungeons and less sailing.

Skyward Sword. It was different, had incredible pacing, and it was just an absolute joy to play (except for when the controls fudged up, haha). I love that game so much.

I don't think I have a favorite, they're all so amazing. I'm loving Skyward Sword so far.

For me I'd say Wind Waker, due in part by nostalgia. It was my first Zelda game, and in my opinion has to this day the most fluid animation and gameplay in all the Zelda games, even better than Skyward Sword. It also had an incredible atmosphere to the game, and had the greatest emphasis on exploration in the entire series imo. I consider it to be the "Exploration" Zelda game, with its massive amount of islands to explore and secrets to hunt down. It truly made me feel like I was on a quest to find the secrets of the world in Wind Waker. The only downside I could find was the fact that it was relatively short compared to TP and SS.

Twilight Princess also deserves a mention (which is actually 4th on my favorite Zelda games list, behind Link's Awakening and Ocarina of Time), as I feel it was the one Zelda game that truly felt "Epic". While it had its flaws (playing as a wolf was quite a drag; the Twilight Realm was pretty bleh), it was still nonetheless a great game with a great storyline and loads of secrets to be found on the overworld, much like Wind Waker.

i'd say wind waker since its style were cool, somewhere between childish and stylish. gameplay were quite good, i hop there is more game made like this

Minish Cap.

It's my favourite because I much prefer 2D Zelda's to 3D ones, as more can be fit in and the experience is just better in my opinion. Minish Cap was the best for me because (although it was somewhat short) it was a very open world - and the distractions such as Kinstone pieces and Figurines were always fun to do, and had an effect no matter where or when you were in the game. Not to mention Ezlo was the best companion ever - he was funny, adorable, and always chimed in with something useful, but never so much that it had you annoyed. The graphics were a nice style, and were very good for the system the game was on, and completing everything took a while, even if the main storyline didnt, and remained entertaining until the very end.

Also, no, I havent just played a few Zelda games.
Ocarina of Time honestly had me bored after a while. The open world was empty and dull - walking around Hyrule field made me just feel amazed at how little they'd added to the environment, and this tends to be my problem with the 3D Zelda's - they use larger worlds and have longer games but the worlds are empty and the games become boring. A game that is short but excellent all the way through is always better than a longer game that gets boring after a while.

I personally love Majora's Mask, now I used to play it on the 64 when I was like 7 so I only enjoyed like the masks and stuff, but I know the story and would love to play it on the 3DS. It was a joy to finally play OoT on the 3DS because I have never played it, So I owuld love to expreience Majoras Mask again

I liked many of the games so I did this:

The Legend of Zelda - All Forest Dungeon Themes

NIER. Though 3D Dot Game Heroes comes pretty close.
_{Okami is a close third, and Zelda: MM would be my fourth favorite}

i say ocarina of time it was my first zelda game and my favorite it had amazing music lots of fun dungeons and amazing bosses

Windwaker is easily not only my favorite 3D Zelda game, but my favorite Zelda game period. There was this charm about Windwaker that I just love so much. I love the art style, I love the gameplay, I love the sailing.

Honestly, it was one of the only games I wanted Nintendo to make for the New Play Control for Wii. I could only imagine finally being able to use the Wii Remote to control the Windwaker.

Skyward Sword was so fun and simple for me, who was using this game to jump into the Zelda series.

I'd say the original, but a big Cowabunga chunk of that is due to that oh so sweet nostalgia. I'll never forget entering the first dungeon for the first time and hearing this little particular icredible tune.....it was 89', I was 5, it was late at night, i was in the dark, by myself, in my room being instantly awe struck by the mesmerizing, eerie, mysterious and gloomy music that perfectly captured the 8-bit amtosphere to the point where i was even a tad frightened to continue.

But if i were to zap that nostalgia way, the amazing time period it was released in(caught it a few years after it's release sadly), and the fact that it was so blippin' amazing during the time I'd have to say that Link's Awakening is the best 2D Zelda. That may change once i plow through ALTTP and possibly The Minish Cap. Meanwhile on the funky man flippity' side, 'Skyward sword' looks too bloody amazing for words.

Definitely Twilight Princess for me. It took everything that made Ocarina of Time great and expanded upon it. The dungeons were bigger, they were harder, the items were used in truly unique ways, and the overworld that gave you that breather was massive without being barren, and it didn't feel like it took forever to get anywhere, unlike Wind Waker, which I would otherwise say is my favorite. Also, it had by and far the most interesting "sidekick" with Midna, who was actually interesting and didn't get in the way, unlike Navi who was super annoying and Phi/Fi (don't know how to spell) who only liked to state the obvious (there is a good chance that the chest over there that is more elegantly designed then the other chests has something important in it. You don't say?) I will say that the boat in Wind Waker and Terra were definitely a step up from Navi too. Also, fishing. You know a game is awesome when you can play a minigame within it for hours. I also loved the dark change in direction for the series.
Now that I think about it, Wind Waker is my second favorite, and it'd probably be a tie if it weren't for the overly barren ocean and the lack of challenge. Also, I find Skyward Sword to be slightly overated, mostly for its pacing, since it didn't really have those breather moments that OOT, WW and TP had. It was do a dungeon, find out where next dungeon is, go through overworld that might as well be a dungeon, do a dungeon, repeat. Yeah, it was all expertly designed, and very fun as well, but I just couldn't plow through it because I wanted to just let go for a bit to give my brain a rest.
Still, every Zelda game from A Link To The Past onward, barring the CDi games, I'd rate at least a 9.5. It's just that good of a series.

Obviously, by my avatar my favorite game is the wand of gamelon. But jokes aside, MAJORA'S MASK!