Spoilers for Watchmen (comic book
and film) to follow.
"do motivations justify actions?"
I think this is what we need to keep in mind here. We have to look at two different things. Motivation and methods. If we operate with a binary worldview (good or bad, nothing in-between) that gives us four different possible outcomes.
Motivation is good, methods are good. This is
Superman. His motivation is completely altruistic, and he has a strict code of honor, which means that he never kills, even if it would save the lives of countless other people. This is as good as it gets.
Motivation is bad, methods are good. This is
Lex Luthor, at least when he isn't actively trying to kill Superman. Luthor (at least from 1986 to 2006) was always characterized as a man motivated by his vanity and greed. He wanted to be the richest, most popular man on the planet. And how did he do it? By donating to charity, by employing millions of people, by throwing fundraisers and everything. Of course, then came Superman and stole his spotlight, which prompted Luthor to create killer robots, evil clones and the whole she-bang. But outside of his personal war with the Kryptonian, he did good things. And yet - if the apple is rotten at the core, it's hard to call it good.
Motivation is good, methods are bad. This is
Ozymandias from Watchmen. His motivation is world peace and an end to the Cold War. He achieves that over the course of the story (though one could argue that the final image will end this short period of peace), but his methods are despicable. In the comic book, he kidnaps scientists, science-fiction writers and artists to create something that kills millions of people. In the movie, he doesn't kidnap them, but kills even more people and frames one of his best friends in the process. This is Evil.
Motivation is bad, methods are bad. This is
Hitler. His motivation was a massive superiority complex, paired with rampant xenophobia and homophobia. His methods were a war of aggression (that eventually drew in the whole world), concentration camps and the Gestapo. This is Evil.
In the case of Ganondorf, he likes to paint himself as an Ozymandias, doing everything he does for the greater good. This is most obvious in, but not limited to Wind Waker. However, if we truly look at it, his motivation is a lot closer to that of Hitler. Sure, it was unfair that the Gerudos had to live in the brutal desert. But that wasn't Ganondorf's only motivation. That was just the front. At the core of it, he was a power-hungry king that wanted to rule over more than just his desert. Besides, just like the Treaty of Versailles, whatever banned the Gerudos to the desert did not justify mass murder and war. And even if he was the poor, tortured soul that he considers himself to be in Wind Waker... he transformed a beautiful land into hell and made himself the king. And then, with all the power of the Triforce, did he transform the Haunted Wasteland into a Garden of Eden? No.
Make no mistake, Ganondorf is as evil as it gets.