Well, this thread's already way off-topic, so I thought I'd throw in my opinion for the heck of it. (Keep in mind it is my opinion, and if your opinion differs, this isn't meant to be insulting.)
I have a hard time comparing OOT and MM because they were both so good IMO, but I'd probably have to say OOT was my favorite because it held more true to the Zelda name as far as its plot was concerned. I still really liked MM for its originality and the hint that another sequel would follow in which Link continued his search for his long lost friend, but I wish the game had been a bit longer than four major dungeons.
WW was definitely not my favorite, though I don't consider it a complete failure. The game was fairly enjoyable - enough that I was willing to play through it more than once. But I have to agree with Clements that the endless (and for the most part, empty) sea was very monotonous. The cel-shaded graphics didn't really bug me too much, but I would definitely have liked it better with OOT/MM-ish graphics. WW didn't seem to have enough "darkness" to it either. In OOT after Link traveled forward in time it was obvious that something had to be done about Ganondorf - he had laid waste to Hyrule. Similarly, in MM all you had to do was look up into the sky to see that the world was in big trouble. For the most part, WW just seemed cheery for a majority of the game. Sure, the dungeons had plenty of puzzles to solve and even creepy parts to them, but there never seemed to be a *global threat* visible that had to be dealt with, just a 1,000+ year old king/boat sending you on missions.
From the looks of things, Zelda 2005 will be more OOT-ish, which I'm really looking forward to. Hopefully Nintendo won't botch it up.