My favourite is definitely Twilight Princess, I've probably explained why multiple times, so I'll keep it simple here.
A lot of my reasoning is down to that great nostalgic feeling, my first true Zelda experience and the game that made me a fan. Ultimately it's one of those special games to me, even if the game was horribly bad in hindsight, I'd still love it. However, I still think it's the best, as I said before, I will have some biased towards this game but I do actually think it's the greatest in the series thus far despite its many flaws.
I'm quite a fan of the darkish theme and and I appreciate it's realism - definitely the most realistic, visuall, so far. It just engaged me more as a player. This combined with a great story, large and diverse overworld, range of dungeons, simply stunning soundtrack and great combat - made this my all time favourite. However, most of my reasoning for why I think it's the best comes from the fact that I feel there's so much potential, essentially this is the perfect template in which to go off and--even with its flaws--I still feel it's strengths bring the game to the series peak.