The Ocarina of Time/ Majora's Mask Link. He is awesome, and he is also the hero of time. He could transform into the many different races of hyrule, and he could become a adult. I grew up on this Link, and he is... well as said, awesome.
Wind Waker Link, and the ONLY reason for that is because the Master Sword he wields in the game is just plain awesome; it's short and broad, and I find that more enticing than the long Master Swords for some reason.
i must admit my favorite link was the minish cap link and the story made sense as he at the start was friends with zelda
also i liked his expressions like when he was with his cap ezlo and the talking cap rather than an annoying fairy and even you could fly with the cap! http://somethingdreadful.net/MeccaPrime/mc/mc5update.png