Most people will say Ocarina of Time but IMO it's overrated. Majora's Mask is the superior N64 game while Twilight Princess is kind of an upgraded version of OoT.
The best Zelda game for me would be Skyward Sword. It's not the hardest Zelda game, but it's visually gorgeous.
RE: What's your favourite Legend of Zelda game and why?
For me I would go for Majora's mask, it had a good story that was quite dark for a game directed to kids like, you that the habitants of clock town are afraid of the moon that will soon hit the small town and some try to ignore the gigantic weird looking moon above their head. Also the Happy mask sellsman is quite frightening