you just said it! "...but with 3D graphics..."

My favorite 3-D Zelda would be Majora's Mask. One of the best N64 games I laid eyes on.

A think a poll is in order, eh?

Wind Waker because of its insane amount of extras

The Legend Of Zelda:Majora's Mask

Ocarina of Time for sure

Wind Waker, hands down. Unique visuals which are stunning, the sailing is fun and relaxing (usually), the music is amazing, the story is pretty damn good. There's nothing bad I can say about this game. Nothing.

After that'd be Twilight Princess, Ocarina of Time then Majora's Mask. MM was awesome, but far too short and easy for me. I completed the game (every heart piece, all items, etc) on my very first time playing in less than a week. Great game, but disappointing compared to other zelda titles.

Majora's Mask. I never tire of saying.

Majora's Mask, although I haven't played Twilight Princess really. Based on what I've heard, my choice is most likely secure.

Twilight Princess definitely.
After that would be Ocarina of Time. Awesome game!

Phantom Hourglass for sure.

Ocarina is my favorite overall, however Majora is pretty close and is in my opinion essential after completing Ocarina, the 2 games are very different and very complimenary to one another, as for Twilight it brought improvements to series such as horse riding and combat, great story and characters too.

Hands down is my first production copy of Zelda: Ocarina of Time signed by the legendary Shigeru Miyamoto.
Just like Mario 64 wowed me with its tight 3-D gameplay - so did "Zelda 64". There was many sleepless nights
playing this game. 10 years later after beating Ocarina the battery is still holding my game saves

@Grooveraider

Wow a signed copy of Ocarina! I got mine on launch day but it didn't have master miyamoto's signiture. I envy you man.
I remember staying awake for nearly three days straight playing that game. Then I fell asleep with the controller in my hand. I was surprised my N64 didn't blow up. I also got Majora on launch day. Ahh the memories.

the same can be said for Ocarina of time, being a cheap rehash of A link to the past.

Wind Waker, but after that it's hard to rank. They're all so amazing.

I've heard it time and again that OoT is Link to the Past in 3D, but it really isn't. No explanation for this has ever been remotely satisfying.

OoT, then TP, WW, and MM. I don't consider PH to be a true 3D zelda game because it is played from a top down view, just like the 2D zelda games.

So what I'm gathering from this thread is...

Phantom Hourglass isn't a 3D Zelda because it's just like the 2D Zelda's... except that it's in 3D.

Because I'm not nuts, I'll stick with saying that Hourglass is 3D... since it is 3D and all.

Well, to a small extent there is 3D action in the other 3D Zeldas (shooting a switch high on a wall and the occasional wall-climbing section), unlike PH, which must be what they meant. But it's almost negligible. Ocarina would not take much mental effort to redesign for 2D space.

Plus, PH is closer in game design to the other 3D Zeldas, anyway. Dungeons are made up of only a few, large rooms. The challenge is derived mostly from puzzles. And it's not particularly good. Etc.

Still, I'd take PH, too, solely because of multi-player, which hopefully Spirit Tracks can top.