OoT is my favorite because well I haven't finish Twilight Princess yet but I LOVED the story and intricacy of OoT, it's very important in the overall story of Zelda, the music and artwork is beautiful (for 64-bit in terms of art), and I just LOVE it! It has personal significance to me as well...
Ocarina of Time and Twilight Princess. I'm not very far at all in Twilight Princess but it's incredible so far! I can't wait to play more of it! The graphics are amazing!