I liked him most in The Wind Waker. He made some awesome speeches, yo. ;o
TWW really defined his character. Before OoT, all we knew him as was this power-hungry, stereotypical villain. In OoT, we saw him as a greedy human with a goal. In TWW, the reasons for that goal were defined, and we saw more into his human side. He didn't start out evil. His people were suffering, and he coveted Hyrule's prosperity. He wanted "that wind". But his needs turned to greed, and he was too weak on the inside. He was twisted by his own greed. He became a a kidnapper and a murderer. But that hint of morality was still there. There was a sadness to him, and I saw that most in his speeches and in that scene where he sat by the sleeping Princess Zelda's bedside. He could have killed her, but he did not. He still had that goal- he needed to confront Link in order to confront himself. In his own opinion, it was too late for him to change, and that goal of obtaining the Triforce was the only thing he had left.
Pretty sad. But he's still pretty ruthless. It's great to see our evil villain have depth to his character.