I notice in a lot of media there is a strong emphasis on the greatness of evil characters. They can often end up more popular than the good guys in the book or on the show, and overshadow everyone else around them.
Darth Vader is a good example. He is a despicable human being who has committed genocide and is responsible for the deaths of billions of people. Yet the common talk is of how much of a badass he is. His coolness has made him one of the most popular characters in history. He is on lunchboxes and has action figures, and people dress up as him in costumes.
How can you write an evil character while reminding the reader that he leaves behind real damage? That he causes suffering and pain to flesh and bone people without dwelling on how awesome he is while doing it?
First of all, I'm a cynic and a misanthrope. But I don't believe in evil. Evil, in my experience, is just a convenient way to dismiss the reality that other people have wants and needs and lived realities that aren't in sync with ours. That's not to say I don't believe in right and wrong--I do. There are things that are not okay and will never be okay no matter what your reasons for doing them. But the people who do them do them because they believe it *is* okay, and that idea comes from other people or from within them, not from some cosmic force whispering in their ear. Calling them "evil," in my opinion, is a way of giving them a pass. Darth Vader is actually a great example here. The prequels showed us why he did what he did and how he became what he did. It wasn't a result of evil. It was real, human decisions, driven by every small, shriveled emotion the human heart has, from selfishness and greed to fear and helplessness. Darth Vader *is* a villain, and did terrible things, but he is not evil. He is human, and that is much more dangerous.
On to the question.
In some genres, in some respect, your villain will always be seen as a badass. That's because villains in a certain kind of book must be highly competent at some things that are pretty cool, like magic and combat and getting their way, in order to pose a threat to your hero. A certain breed of fan will always equate that with badass.
But such villains *can* be managed and, if that's the desire, avoided. They tend to show up, as my memory tells me, in larger than life stories, with archetypal characters. The more human reality in the story, the less iconic or "sexy" the villain. Voldemort will always have his fans, and this isn't the place to debate Snape, but Ben Ladradun (Cold Fire by Tamora Pierce) is a small, pitiable man who was selfish enough to think the world owed him.
Part of what I'm seeing looking at my bookshelf is that the key to making a villain less "sexy" is making them less "evil." None of my own books have "evil" antagonists; most of them don't have "villains" at all. Snyder thinks he's looking out for Alec; Lindsey is trying to save her son from the fate our protagonist's father left him to. There is something small and scared at the core of such people, something that stops them from being "sexy."
Of course, it is pretty cool that Lindsey can rip out your still-beating heart and leave your skin intact.
The alternative, of course, is to make them MORE "evil." Check TV Tropes for Moral Event Horizon. Empress Berenene dor Ocmore (Will of the Empress, Tamora Pierce) is a wonderfully written villain and has beautiful shades of humanity woven through her--but I hate her because she condones the forced marriage of women in her country. In one of the fanfictions I'm writing for Kingdom Hearts, even if it was original and even though it's a fairly popular villain, no one would root for him as I've written him, because for ten chapters before we even learn his name we watch his victim struggle through panic attacks and flashbacks relating to the abuse they suffered at his hands.
And oddly enough, no, genocide and murder won't be that Moral Event Horizon, unless the genocide is of a group we're inclined to protect. Blowing up a random planet we don't care about = eh, for all we know it was a prison colony. Active affiliation with Nazis = your villain is now dead to almost all your readers.
(All of the above, of course, is my own opinion, based on what I've read and observed while reading and writing.)