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Woo, another meme! Gotta say, this one was a LOT harder than the last; I've got a huge list of honorable mentions before explaining the main list (and a lot of them nearly made the 10th slot but I was too lazy to swap it out)

Grand Admiral Thrawn- (Star Wars Heir to the Empire)- He's a brilliant tactician who figures out the enemy by studying their art
Giygas- (Earthbound)- I've only played this game once, but once is enough... knowing that Giygas' dialogue was based on a rape scene just makes the boss more intense (I know it wasn't really a rape scene, but the game's director thought it was, so the effect was real in his mind)
Deathborn- (F-Zero GX)- While only appearing briefly, I love Deathborn's exposed-brain helmet, sinister eyes, and ability to make Black Shadow cry like a little girl
Mewtwo- (Pokemon Red/Blue)- Smash Bros Melee calls him a villain, and he's always been one of my favorite pokemon
Majora- (Zelda Majora's Mask)- the insane, mutating mask that calls down the moon... awesome
Ganondorf/Demise- (Zelda series)- classic villain, and his look in Skyward Sword was really cool
Darth Nihilus- (Star Wars KotOR II)- While he doesn't do much, the fact that Nihilus died and continues to preserve his soul by bonding it to his own armor, transforming himself into an endless hunger for Force energy, like a black whole consuming everything, makes him really epic as a villain. He's like a force of nature.
Slade- (Teen Titans)- It's been a long time since I saw this show, but I always loved Slade... he was so mysterious; his mask cracked but his face was always hidden.
Discord- (My Little Pony)- Yes, that pony show. Thematically, I love how Discord was able to pick apart all the values the ponies cling to and turn them upsidedown, destroying everything established in the first season.
Venom- (Spiderman)- Venom's interesting because he's developed from a vengeful villain into more of an antihero, sharing Spiderman's sense of justice for protecting the innocent (though regarding Spidey himself as far from innocent). The suit itself acts like a scorned lover, constantly pursuing Spiderman to get back to him, or get back at him
Dark Samus- (Metroid Prime series)- Dark Samus never speaks, but it's awesome knowing she's really Metroid Prime, so it's like a humanoid metroid.
King Boo- (Luigi's Mansion)- Boos are so cute~ It was great to see them get the starring role as baddies in Luigi's Mansion
Marx- (Kirby Super Star)- In his armless form, Marx has to be one of the most adorable villains out there. That jester hat and the little feet bouncing on that ball... I really didn't see his betrayal coming, but that was pretty epic too.

Also these all had to be animated, so that cut out some of my other choices

10- Carnage- (Spiderman series)- Between Venom and Carnage, I prefer Carnage for looks, and he's more of a villain than Venom in that he's insane and void of a moral conscience. [link]

9- Wilfre- (Drawn to Life series)- Besides being an adorable little shadow rabbit blob thing, I found Wilfre really compelling as a villain. I love the way his music sets the tone for his scenes, how he talks calmly to the hero, always appearing to know something that no one else has realized yet. Especially in DTL2... by the end I was ready to take his side and fight the raposa, knowing that they intended to destroy the world to save some kid I don't even know. [link]

8- General Grievous- (Star Wars Clone Wars)- Just Clone Wars, not Episode III, not The Clone Wars. When Grievous took on six Jedi at once at the end of Clone Wars volume I, that battle became the most epic villain scene of my childhood. Then George Lucas castrated him into a "villain who runs away" [link]

7- Darth Vader- (Star Wars series)- Since this has to be an animated list, I'm focusing on his appearance in Force Unleashed I/II. Especially in II, that scene where he repeats "SHE DIES" is pretty intense [link]

6- Magneto- (X-Men)- Admittedly, I'm more familiar with Magneto from the movies, but I still love him in concept: the ways in which magnetism is utilized in his stories is pretty fun, and that mask gets more epic when shadows are animated in. [link]

5- Darth Bane- (Star Wars)- While he's more from books, he was also in some comics, so he counts. Darth Bane's compelling because he's a philosophical Sith; he didn't delve into the dark side on some mad, passionate quest for power, but because it was the logical thing to do in a galaxy at war. For him, it was a matter of a powerful individual maximizing his power, even when it means slaughtering all of his comrades to end their foolish pseudo-Sith. (image from book cover)

4- Zero Two- (Kirby 64)- Reason 1: best Kirby battle theme EVAR. Reason 2: though not fully explored in the game, Zero's name comes from the idea that he exists to destroy all emotion in the universe, reducing it to nothing. He's a greater threat than any of the giant conquerer demons that come to Dreamland, because his goal isn't to rule, but to assimilate everything into his mind-possessing Darkmatter collective (Borg, anyone?) Oh, and he bleeds. In a Kirby game. [link]

3- Mysterio- (Spiderman)- A personal pick here, since as a villain, Mysterio isn't all that great. True, he can mess with Spidey's mind like nobody's business, using holograms and hallucinogens to twist his perspective. What I find interesting about Mysterio is that he has the skill to be a great stage magician, but he chooses crime instead; one story explained that being rich/famous wasn't enough for him, he feels the need to prove himself superior to common people through his crimes. Also, I love that fishbowl, xD (image from google images)

2- Boba Fett- (Star Wars)- Another case where I'm drawing on his comics and games and such. Boba Fett has one of the coolest helmets ever, hands down. As a character, I actually preferred Boba Fett before the clone origin story, but his post-RotJ stories still hold up as portraying him as the cold, calculating bounty hunter. [link]

1- Meta Knight- (Kirby series)- arguably MK is more of an antihero, but I'm citing Revenge of Meta Knight for him as a villain. As games go, that one really shaped my childhood; I've done a full fanfic explaining how Meta could be a villain in that given his otherwise mostly-good appearances, explaining how events in his past led him to it. Meta's been one of my favorite characters for a long time, mostly from the awesome mask and cool, calm demeanor. I geeked out when he was added to Brawl; heck, I geeked when I saw his trophy in Melee! [link]

EDIT: *sigh* I completely forgot MGS when making this list, and that has some of the best villains. Okay:
Grey Fox- a cyborg ninja who becomes your ally; arguably the best cyborg ninja in the series
Ocelot- like Snake, Ocelot gets a lot of development over the series, and you come to learn how his only true loyalty is to Big Boss. He makes himself a trusted ally of major characters through each game, then subsequently betrays each, usually accompanied with an intricate explanation that masks his true motives. As complex villains go, Ocelot is one of the best.
Big Boss- while rather shallow in his early games (as far as I can tell), by the time we see him in MGS3, Big Boss becomes incredibly sympathetic. We see how the government betrayed him and why he felt it necessary to create his private military state, and his self-analytical comments at the end of MGS4 solidifies him as a truly intriguing villain

Description
Original: [link]

Woo, another meme! Gotta say, this one was a LOT harder than the last; I've got a huge list of honorable mentions before explaining the main list (and a lot of them nearly made the 10th slot but I was too lazy to swap it out)

Grand Admiral Thrawn- (Star Wars Heir to the Empire)- He's a brilliant tactician who figures out the enemy by studying their art
Giygas- (Earthbound)- I've only played this game once, but once is enough... knowing that Giygas' dialogue was based on a rape scene just makes the boss more intense (I know it wasn't really a rape scene, but the game's director thought it was, so the effect was real in his mind)
Deathborn- (F-Zero GX)- While only appearing briefly, I love Deathborn's exposed-brain helmet, sinister eyes, and ability to make Black Shadow cry like a little girl
Mewtwo- (Pokemon Red/Blue)- Smash Bros Melee calls him a villain, and he's always been one of my favorite pokemon
Majora- (Zelda Majora's Mask)- the insane, mutating mask that calls down the moon... awesome
Ganondorf/Demise- (Zelda series)- classic villain, and his look in Skyward Sword was really cool
Darth Nihilus- (Star Wars KotOR II)- While he doesn't do much, the fact that Nihilus died and continues to preserve his soul by bonding it to his own armor, transforming himself into an endless hunger for Force energy, like a black whole consuming everything, makes him really epic as a villain. He's like a force of nature.
Slade- (Teen Titans)- It's been a long time since I saw this show, but I always loved Slade... he was so mysterious; his mask cracked but his face was always hidden.
Discord- (My Little Pony)- Yes, that pony show. Thematically, I love how Discord was able to pick apart all the values the ponies cling to and turn them upsidedown, destroying everything established in the first season.
Venom- (Spiderman)- Venom's interesting because he's developed from a vengeful villain into more of an antihero, sharing Spiderman's sense of justice for protecting the innocent (though regarding Spidey himself as far from innocent). The suit itself acts like a scorned lover, constantly pursuing Spiderman to get back to him, or get back at him
Dark Samus- (Metroid Prime series)- Dark Samus never speaks, but it's awesome knowing she's really Metroid Prime, so it's like a humanoid metroid.
King Boo- (Luigi's Mansion)- Boos are so cute~ It was great to see them get the starring role as baddies in Luigi's Mansion
Marx- (Kirby Super Star)- In his armless form, Marx has to be one of the most adorable villains out there. That jester hat and the little feet bouncing on that ball... I really didn't see his betrayal coming, but that was pretty epic too.

Also these all had to be animated, so that cut out some of my other choices

10- Carnage- (Spiderman series)- Between Venom and Carnage, I prefer Carnage for looks, and he's more of a villain than Venom in that he's insane and void of a moral conscience. [link]

9- Wilfre- (Drawn to Life series)- Besides being an adorable little shadow rabbit blob thing, I found Wilfre really compelling as a villain. I love the way his music sets the tone for his scenes, how he talks calmly to the hero, always appearing to know something that no one else has realized yet. Especially in DTL2... by the end I was ready to take his side and fight the raposa, knowing that they intended to destroy the world to save some kid I don't even know. [link]

8- General Grievous- (Star Wars Clone Wars)- Just Clone Wars, not Episode III, not The Clone Wars. When Grievous took on six Jedi at once at the end of Clone Wars volume I, that battle became the most epic villain scene of my childhood. Then George Lucas castrated him into a "villain who runs away" [link]

7- Darth Vader- (Star Wars series)- Since this has to be an animated list, I'm focusing on his appearance in Force Unleashed I/II. Especially in II, that scene where he repeats "SHE DIES" is pretty intense [link]

6- Magneto- (X-Men)- Admittedly, I'm more familiar with Magneto from the movies, but I still love him in concept: the ways in which magnetism is utilized in his stories is pretty fun, and that mask gets more epic when shadows are animated in. [link]

5- Darth Bane- (Star Wars)- While he's more from books, he was also in some comics, so he counts. Darth Bane's compelling because he's a philosophical Sith; he didn't delve into the dark side on some mad, passionate quest for power, but because it was the logical thing to do in a galaxy at war. For him, it was a matter of a powerful individual maximizing his power, even when it means slaughtering all of his comrades to end their foolish pseudo-Sith. (image from book cover)

4- Zero Two- (Kirby 64)- Reason 1: best Kirby battle theme EVAR. Reason 2: though not fully explored in the game, Zero's name comes from the idea that he exists to destroy all emotion in the universe, reducing it to nothing. He's a greater threat than any of the giant conquerer demons that come to Dreamland, because his goal isn't to rule, but to assimilate everything into his mind-possessing Darkmatter collective (Borg, anyone?) Oh, and he bleeds. In a Kirby game. [link]

3- Mysterio- (Spiderman)- A personal pick here, since as a villain, Mysterio isn't all that great. True, he can mess with Spidey's mind like nobody's business, using holograms and hallucinogens to twist his perspective. What I find interesting about Mysterio is that he has the skill to be a great stage magician, but he chooses crime instead; one story explained that being rich/famous wasn't enough for him, he feels the need to prove himself superior to common people through his crimes. Also, I love that fishbowl, xD (image from google images)

2- Boba Fett- (Star Wars)- Another case where I'm drawing on his comics and games and such. Boba Fett has one of the coolest helmets ever, hands down. As a character, I actually preferred Boba Fett before the clone origin story, but his post-RotJ stories still hold up as portraying him as the cold, calculating bounty hunter. [link]

1- Meta Knight- (Kirby series)- arguably MK is more of an antihero, but I'm citing Revenge of Meta Knight for him as a villain. As games go, that one really shaped my childhood; I've done a full fanfic explaining how Meta could be a villain in that given his otherwise mostly-good appearances, explaining how events in his past led him to it. Meta's been one of my favorite characters for a long time, mostly from the awesome mask and cool, calm demeanor. I geeked out when he was added to Brawl; heck, I geeked when I saw his trophy in Melee! [link]

EDIT: *sigh* I completely forgot MGS when making this list, and that has some of the best villains. Okay:
Grey Fox- a cyborg ninja who becomes your ally; arguably the best cyborg ninja in the series
Ocelot- like Snake, Ocelot gets a lot of development over the series, and you come to learn how his only true loyalty is to Big Boss. He makes himself a trusted ally of major characters through each game, then subsequently betrays each, usually accompanied with an intricate explanation that masks his true motives. As complex villains go, Ocelot is one of the best.
Big Boss- while rather shallow in his early games (as far as I can tell), by the time we see him in MGS3, Big Boss becomes incredibly sympathetic. We see how the government betrayed him and why he felt it necessary to create his private military state, and his self-analytical comments at the end of MGS4 solidifies him as a truly intriguing villain