I voted Twilight Princess. The main reason why is that for me it had a much more mature take on the Zelda series (if still childish at times) which I personally preferred. Not just in terms of graphics, but the fantasy devices used (Link as a wolf/twilight realm), the reactions of characters, and the events of the game.
Hell, even the concept art was much more mature. Here's Link in OoT:
And from MM:
And now from TP (sorry for bigness):
See what I mean? See how much more badass he is the TP one?
Anywho, I've always found the Zelda series a bit childish (as much as I like it

), and if Nintendo keeps taking the series in the direction of TP then I'm sure the next game will be even better (I'm not counting the DS titles by the way - for me 'console' Zeldas are the only true titles).
And if I could get a vote for second best, it would of course be OoT.
/rant