Which is the best?
I say Link to the Past. It just had everything I'd ever want in a Zelda game, hard bosses, long dungeons, a huge world, and actually decent puzzles.
Close behind I'd say Link the the Past(DX or not). It was a little lacking, but the one thing that it had that I haven't felt in any of the other Zeldas, was it had actually fun puzzles. Zelda isn't the greatest when it comes to puzzles, same old shoot the eye or get the key...but this was so much better.
Windwaker would be next, it suffers from the puzzle thing...and...the most hated thing about it for me is the damn ocean. It just gets SOOO boring. It's vast, and has nothing to do in it. Morrowind suffred from this too, but usually you had the option of Slit Sliders and the magic guild at least. v_v
OOT would follow, I guess. This game was just too...ehhh...bland. Great game, but it's not the best. Just...yeah...
All the others, except for the CDI ones, were also great...but too lazy to talk about them.