Emotionally, it's Skyward Sword. Graphics-wise (not the facial expressions, just overall color scheme and such), it's Twilight Princess. Top two Link's, though TP's probably my fave. Third place goes to Ocarina of Time/Majora's Mask, definitely.
Well my first ever Zelda game I played was Ocarina of time, so I grew up with that Link..
but I also really like the Skyward Sword and Twilight Princess Link due to their emotions and improved body language and graphics. :p
Wind Waker Link, he seemed to be pretty bemused by the fact he was saving the world. Then, Twilight Princess Link he didn't even know what was going on, got transformed into a shadow wolf and then saved two princesses.
Since you play out a story from Link's point of view, this is almost like saying "which game is your favourite?" Almost. However, I'm still sticking with Ocarina of Time's Link, due to his relationships between each of the sages and their people. The connection I felt as a player was more than in any other game.
For the longest time it was either the Hero of Wind, or the Hero of Time. They have both gone through so much that you know that their outstanding people. Ever since Skyward Sword, there was no competition. He displayed his emotions without it being overpowering, and I think he really embodies the essence of Link the most. He really is how I would imagine all other Link's. He is also one of the most courageous Link's in my opinion. He looked down the ultimate embodiment of evil, gave him one heck of a look and drew his sword. It. Was. Awesome.