Evil ranking:
10) King Dedede - Only really here because he's considered a villain in stuff like Smash Events, but he really does not classify as a villain at all at this point in the Kirby series)
9) Mewtwo - Sort of a similar deal. He killed some people, sure, but they were in the wrong anyway. Other than that, anime Mewtwo was simply misunderstood and turned over a new leaf anyway (just going by the first movie here). Game Mewtwo in Gen 1 was literally just the ultimate prize, once caught he serves the protagonist so it's hard to call him evil at all at that point. He's much closer to an anti-hero in general.
8) Wolf - Again, more anti-hero. He's a mercenary, so he goes where the money is at. He doesn't have a grand plan for world domination or have any particularly evil wishes himself, but he is willing to serve under those that do if they pay. His vendetta towards Fox is a personal thing, and he has willingly helped Fox before too, so despite being an enemy to the hero on most occasions, that alone doesn't really make him a villain considering the circumstances.
7) Andross - Actual villain of the Star Fox franchise so yeah he's evil. Not particularly threatening though, and Zero tried to give him a "misunderstood" angle too (though it was poorly executed).
6) Bowser - THE video game villain, so you'd think he'd be higher. But really, for the most part his plans are so basic and easily foiled that he's not that threatening and he's most often portrayed as a lovable goofball more than he is a genuinely threatening villain. Most boss fights against him are also super easy too. He also has a fair few redeeming qualities, like being a genuinely loving father and having a genuine love and care for Peach. He has also helped Mario on occasion against truly evil threats. The most evil he has ever come across is in Galaxy (oh, and Brawl), but it was quite poorly executed (and Rosalina seemed to think he was good enough to revive anyway). At the end of day, he still gets invited for a round of golf or kart racing every time anyway. He's only really this high because he's the first character you think of when it comes to video game antagonists.
5) Dr. Wily - Crazy mad scientist who does what he does purely out of revenge, spite, and self-pity. Some of his plots are pretty diabolical too, like the Roboenza (sp?) one. However, he is quite the coward and can be really pathetic without his machines. And he ultimately only does what he does to spite Dr. Light.
4) King Garon - Really sick and twisted man. Haven't actually finished Birthright just yet, let alone the others, but he causes immense suffering for loads of people, Nohr is basically a ****hole by the looks of it because he does not care to look after it, and even his own children fear him. While he may have some noble cause behind everything that I don't know about yet, he's definitely one of the most cruel villains Nintendo has created on his deeds alone.
3) Ganondorf - Kinda like King Garon really. Not much else to say honestly. In fact, I would actually put King Garon above him if it weren't for the fact Ganondorf has been in way more games, and the fact that Ganondorf has a much longer life in canon (unless I haven't discovered something about Garon yet - please don't hint towards it if that is the case). But yeah, needless to say, he didn't get the title of "King of Evil" by pickpocketing a few Hylians.
2) Hades - KI:U Hades is just a complete sociopath, with a lot of power. He's messed up, to the point of hilarity. He literally eats the souls of the dead for breakfast. He really doesn't care for anyone and has no fear, to the point where he will make casual conversation with the protagonist, that's how non-chalant he is. Would be #1 but he only had a presence in one game. But that was a good enough role to sky rocket him to #2.
1) Dr. Eggman - He's basically a mortal equivalent to Hades. But that doesn't make him lesser, for he has himself TAMED immortal gods to do his bidding. Eggman has but one dream, and that is for the world to acknowledge his genius. And he will go above in beyond in making people respect him. He broke the planet apart to summon an apocalyptic god, JUST so he could build and power a theme park! That alone is enough to convince me. He's done so much more too, from enslaving innocent animals, capturing an alien race and harvesting them for energy, and so on and so forth. His only folly is his own madness and pride, which cause him to make one small mistake that ruins everything in his plans. While he has had goofier and less evil portrayals (Sonic Boom makes him like Dedede, for example), most game portrayals keep him quite intimidating, and his plans are always bombastic and over the top. What makes Eggman stand out as a villain is that, his GOALS may not be as pure evil as someone like Hades, but his METHODS are, if not worse. That makes him #1 for me, I tend to think evil deeds are worse when the reasoning is more on the petty side. Ganondorf, for example, does horrible things, but he needs to, as he has big plans and has some genuine reasons for wanting to do those things. Dr. Eggman has done even worse things than Ganondorf though, but he doesn't have a hint of a noble cause, it's not even really about ruling a kingdom or anything, he just wants to make people think he is the greatest man in the world. Which just makes him the #1 for me. With an IQ of 300 and the physical fitness to compete in the Olympics, he's definitely got the abilities to back himself up, too.