In this, I will be ranking them based on their relationships with their nemeses/nemesis, their actual game, and a the lore of the characters.
He's a sorry excuse for a villain. He's literally just a minor enemy to avoid from. He's just..not important.
He's probably just jealous or mario. He's annoying as the devil himself, and is for some reason in the game, but no Waluigi. He's not as good as a villain as some of the others, but better than the P L A N T.
He's Fox's main arch-nemisis, after being beaten so many times. He attacks Fox for personal revenge after failing his original mission to capture him. Not much else is known about him though, so he doesn't make it that high up the list.
He is first confronted by Kirby due to stealing all of Dreamlands food, turning him REALLY fat. He breaks the dream rod, which makes people think he wants them to stop having dreams, when he really was keeping Nightmare locked up in the Fountain of Dreams. He briefly assists Kirby, but goes back to being Kirby's nemesis. He has fought with and against Meta Knight before, but that makes their elationship REALLY confusing. He's just too joyful though, at least, compared to others.
She was born from somethng called, Phazon, which was formed from copying samsu's suit and the metroid's...uh, DNA? I don't know, I forgot my research already. Anyways, she's able to regenerate as long as there is Phazon still around. No matter how many times Samus will kill her, she's always coming back, until there's no Phazon left for her to regenerate.
He's menacing, but just not enough of a reason to be the Kongs' nemesis. He's only his nemesis through a deep grudge, like Wolf, except he ACTUALLY succeeds in kidnapping Donkey Kong, leaving Diddy to save him. Their relationship is basic, but K. Rool is actually really smart. He will trick the player into thinking he's lost, but he will get back up and you have to beat him up a couple more times, then he's dead.
He hates cloud for being just better than him. Cloud's very existance gets on the one-winged angel's nerves. He wouldn't be a villain if he wasn't arrogant. Sephiroth has a decent excuse for his villainy, but he does have a couple of friends, unlike SOME OTHERS.
He has lots of ambitions, such as wanting to rule the world. He goes from a blue hog, to a bat, and finally, to a humanoid. It's intresting how he was originally a normal until he stole something powerful, changing him into a monster. Hey, that sounds a lot like Sméagol! He is always defeated by Link in all the games he is in. He has a basic villainous motive, but a dangerous one.
He's a noble. lonely knight, who teters on the edge of a villain, and a hero. He has many times saved Kirby, but then outright threatens to kill him sometimes. But, he has attempted to protect dreamland many times before, he's not as much of a villain as Bowser or Ganondorf, but he is a good character in general, just not villinous enough.
He was lied to by Bowser that Peach was his mom. So he kidnaps her, as always, and is defeated by Mario. He says when he grows up, he's going to beat up Mario some day. Though he only appears in spinoffs, he still is a decent villain with a decently sad backstory.
He's just a more evil Pit. Though, sometimes he joins Pit in somebattles, and even defeats Pandora to save him. They are basically brothers from another mother, literally. Dark Pit was born from a mirror, and beats up Pit to steal Pandora's powers, but later releases Pandora to fight her and save Pit after Pit saved him. Dark Pit is also known as Pittos, random little fact. Though he may not be the most villainous of the villains here.
He's the OG villain, who want's to marry peach in almost every single game. He goes from turning into a Giant, Giga Bowser, to his normal-self in a wedding suit. He's been mario's nemesis ever since they met. He even hates other like Luigi, Toads, etc. Although, he is a bit too kiddish compared to the #1 spot...
You want gore and suffering? Well sit right up and relax as you are introduced to a nightmare of evil. He's an absolute monster. There's a reason he's named,"Cunning God of Death". Bowser or Ganondorf may be the evilest of villains, but Ridley is on a whole nother level BY HIMSELF. Man traumatized Samus as a THREE-YEAR OLD, by killing her parents, and eating them and her friends to stay alive. He massacres innocent people, as a little happy hobby for himself. Ridley is known to be able to speak and is highly intelligent, hench how he survives the explosion of the ship, by eating her parents and friends. I know right? Dark, even for my main. He has literal Afton material, with the famous line,"I always, come back", which is true. He comes back as Meta-Ridley, Neo-Ridley, and even a robot of himself, which he built. He even comes back for round 2in Super Smash Bros Brawl as a Meta-Ridley boss. His level of evil and trama dealt to his nemesis compared to the other characters is the reason he's #1, not even biased.