Tough call. Very difficult when one game is still fresh in our minds, and other ones seem dated. But than again older games we see through rose-colored glbumes.
LoZ: Link to the Past – Broke pre-conceptions of what a game should be. The world wasnt liner and was wide and open and totally gave a new feel to everything I knew.
OoT – Same idea as above but now walking into the realm of 3D. This was close to being number 1, there wer just a few minor problems I had with it. Perhaps this will take number one on the list depending on my mood.
Majora’s Mask – Debating this or Wind Waker, but seeing as both suffered a “problem” I suppose this would be better. The problem I refer to is having less dungeons that I’m used to. Felt too short in that regard. But very different feel which I find to be … not revolutionary, but it a very cool take on the universe.
Wind Waker – While I wasn’t too keen on the cartoonish feel, it does make up for it in gameplay. Once again, too few dungeons, but some nice side-quests (got all the figurines)
Twlight Princess – Before you kill me for this, I’m not really sure where I should put TP (on the bunghole oh ha ha ha Log in to see images!). The main problem I had with this game was that it didn’t feel like a Zelda game. Don’t ask me why. Srsly don’t. Why so srs?
Loz – Yeah the first one. Just cause.
Adventure of Link: Zelda II – Yes, that was the name of the second game. I truly feel Zelda was not meant to be an RPG. The game had some interesting ideas, but it’s just not suited for Zelda. The map was kinda of interesting althought slightly disjointed. Oh, and look at the town names, and tell me if those don’t look familiar.

I did not include any of the GB, GBA, or DS games as I don’t have them. But I’m pretty sure Link’s Awakening would be on there (even if it has a cliched ending).