Ganondorf. In Wind Waker especially, he comes across as a character almost in need of pity, rather than scorn. Yes, he's an evil super-villain. Yes, he unleashes hordes of monsters. Yes, he keeps trying to conquer the same Kingdom over and over again, endlessly thwarted by a ten year old boy, but despite that there is a side to him that pulls at your heart strings.
My personal theory on Ganondorf is that, like Link and Zelda, he is enslaved to the role he plays. However, whereas each Link and each Zelda endure the saga once, then live out the rest of their lives largely trouble free, Ganondorf is always the same individual; doomed to spend eternity being shot with Light Arrows and stabbed with the Master Sword.
Moreover, since the 'reinventing' of the Series in Ocarina, each character has been bound to a piece of the Triforce. Ganondorf is bound to the Triforce of Power, and he has used that to consume the world in Darkness. One could assume, therefore, that the Triforce itself may exert itself upon him; he is enslaved to the rage and fury that were his strongest traits when he first touched the Triforce, now forever doomed to follow that destructive path.
In the rare moments of lucidity before and after his duels with Link, Ganondorf often appears a sorrowful individual. Born into a harsh, unforgiving land, bound to an endlessly repeating Legend, consumed by powers mortals were never meant to wield, and cursed with immortality to ensure he can never end his forsaken existence.
I feel sorry for Ganondorf.