I've only completed the N64 and NDS Zelda games so far, but I will agree unreservedly that the Legend of Zelda series is one of the three best series in gaming-the other two being Mario and Sonic.
I will say, though, that my favourite so far is Ocarina of Time. And I can sense the hate coming my way for this next bit: I liked the Water Temple, I thought it was fun. There. I said it.
Seriously, though, the Water Temple was a real challenge-and there aren't many of those in Zelda these days. Heck, there aren't that many in videogames anymore, unless you count Mega Man, which is basically one big challenge. Ok, and MAYBE Mario Galaxy and Mario Galaxy 2.
And challenges make a game good. Although the three days mechanic in Majora's Mask did get a bit annoying near the end, it was still a great game nonetheless. Bringing back the Ocarina was a great idea, and the number of Masks is enough to keep anyone satisfied-especially the Fierce Deity one-that gave a reason to go fight all the bosses again, just to try it out!
Moving forward to the DS games, I don't understand why people disliked Phantom Hourglass. It was a great game, and the sailing mechanic, not quite new to the franchise, was still a good addition. The temples were quite well-thought-out, and the final boss was an interesting use of many different gameplay mechanics-including the sailing one mentioned earlier.
Spirit Tracks, though, beat Phantom Hourglass hands-down. Better use of items, better items, better bosses, more collectibles and side-quests, an incredible boss battle-that in fact ranks highly on a top ten Zelda boss list on YouTube-and not forgetting of course the rabbits. I liked that minigame.