I'll pull together a quick list of three: Ganon from the Legends of Zelda (I'm going to start calling it Legends, because each game is pretty much its own legend): He is always such an accomplished villain. He usually leads the Gerudo to be a somewhat thriving society, he's perhaps the greatest wizard in the world (I'd wager he's more magically powerful than Zelda, with or without their triforces), he's such a chessmaster with planning, and he's become immortal partly by his own might. He always gets sealed away, but I'm pretty sure he's still never been killed. Handsome Jack from Borderlands: The king of trash-talk and ego, and surprisingly one of the more understandable villains I've encountered. He's a completely mad maniac and high-functioning psychopath, but he also loves his daughter dearly and will do anything to keep her safe, even if it's not the right thing. Omega from Mega Man Zero: Not only was his final boss fight (spoiler, but it's easy to see it coming from the beginning of the game) one of the most intense video-gaming experiences ever, I loved the message that his encounter has for the theme of the game, which I will boil down to: it doesn't matter what you are, it matters who you are.
Number one for me has gotta be Ridley from the Metroid series. He just has that perfect combination of cunning and brutality; extremely bloodthirsty and violent, but still smart enough to lead the Space Pirate military against the Galactic Federation. He even taunts Samus in in the manga during their fight. Fawful from Mario & Luigi: Bowser's Inside Story is up there two. He's kind of silly and talks in a funny way, but he has this big master plan involving a lot of different moving parts and manages to almost complete it. Throughout the game, he easily manages to take over both Peach's Castle and Bowser Castle (brainwashing all of Bowser's minions in the process), finds and breaks the seal on the Dark Star, and manages to absorb it's power! The only real reason he lost is because Bowser prevented him from absorbing all or it. I won't say who this is because it's a really major spoiler, but the main villain of Stella Glow is really good too. They're trying to wipe out humanity simply because that's what they were created to do. No vendetta. No "I am a higher being that deserves to rule." It's just their purpose in life.
@Negative Zero In one timeline he is dead, like, permanently. Windwaker onward in the Flooded Hyrule timeline has no Ganon as he is dead. The other timelines still has a Ganon though ^^ Comical, yet dangerous, Eggman takes the cake as he has the master plan. Don't you know he hates that disgusting blue hedgehog? Lol. But yes, Eggman is a favorite due to how humorous he can be with/without his robotic henchmen. He does have his serious moments though, and they're very memorable for me (such as when he held Amy at gun point, or completely shattered the earth with Sonic watching-captured and weakened). I can't say anything about 06's version of Eggman (due to me not playing it), but it's a horrible design and I'm glad they didn't stick with it. Ganon is also on my list for all the reasons Negative Zero stated as well. I'm someone who enjoys the lore more than the games (I suck at them), though ^^'' On terms of very dangerous and horrifying villains, Mephiles the Dark is the only extremely dangerous villain I have really known of. A bit of a 'coward', as many put it, he doesn't focus on fighting, himself, but instead tricks others into doing what he wants through manipulation. He also had multiple plans so, in case one fell through he could continue on his ultimate goal easily. Mephiles is also the only villain to actually kill off Sonic- even if it was retconned at the end of the game.
Vayne Solidor. He is easily the greatest Final Fantasy series villain to me, because in any other video game he could easily pass as a protagonist...he'd be a dark protagonist, to be sure, but no darker than, say, Yuri Lowell from Tales of Vesperia, or Velvet Crowe from Tales of Berseria. A complicated man with noble intentions who crosses the line so that his brother doesn't have to. A believable character, in short. One burdened with a pretty daunting task who crosses the moral line where the protagonists do not, which is the sole difference between them in the end. He is a villain solely because he is opposed by the characters that you control, not because he is inherently evil or corrupt, and villains like that are the ones who interest me the most, as they have the most complex motivations and are often more compelling than the protagonists. This could also apply to Venat, who is branded a heretic solely because he is in the minority and actually wants to achieve what the protagonists achieve in the end - mankind's destiny becoming its own once again - but as he is generally a behind-the-scenes villain and not relatable in the same way that Vayne is, I honestly wouldn't consider him on the same sort of level. Also, Zanza from Xenoblade Chronicles, purely because I didn't see it coming. It is so rare these days for me to not see a plot twist like that coming. I can't say I particularly care for the backstory XC2 gave him - because XC2 was a very bad game overall and adding that little Klaus connection did absolutely nothing for him really - but god, was he effective as a villain. ...and I need a complete psycho on this list, so Lezard Valeth gets a special mention. Mild-mannered, extremely helpful Lezard...who manipulates everything and ultimately becomes a God with his own little pocket dimension. It's more his dialogue that gets me, though...his laugh is absolutely terrifying. There's also Meteor Swarm. Liam O'Brien absolutely nails it.
Dr. Wiel from Megaman Zero 3 & 4. Not only does he steal from zero in a way no one saw coming, but he flat out tries to run a space station into the ground from orbit while he is still on it! On top of that his actions affect the entire ZX series! And then there is Dr. Wily. If you look at the story from the classic series all the way to the ZX series, the whole thing is set in motion by doctor Wily. If he hadn't waged his war with Dr. Light, nothing else would have happened after classic. There would never have been mavericks, there would have been no elf wars, and there would be no biometals, he set that entire thing in motion because Dr. Light wouldn't give him credit for his work or something like that. He was a big whiner but man did he have a lasting impact on his world that ran for like 600 years after he died!
I got reminded over this week how much I admire Cyrus from Pokémon Sinnoh as a villain. At the young, young age of 27, this man was running a criminal enterprise underneath the legal front of an energy research firm which is probably also doing legit cutting-edge research (likely led by himself as owner, lead researcher, CEO, CFO, etc), enslaved 4-5 (almost plus one or two more) primordial deities, and got within spitting distance of creating a new universe of his own design with himself as its god. Life goals. I need to get busy. In addition to that, he's rather involved as a villain, almost as good in this regard as Handsome Jack from my previous post. Many villains you never even meet until the final throwdown, but Cyrus you either meet in the first few minutes (Pt) or first few hours (DP), and he remains an active villain from that point forward; and he has actual, tangible, relateable causes for his personality and villainy in the background lore. That's better than Bowser most of the time (no shade to him).
Here goes. Spoiler: Kirby Star Allies/Triple Deluxe, Super Paper Mario, and A Hat in Time - Count Bleck, Super Paper Mario: Dapper, unique, and has quite the backstory. His backstory is well-written, and he's proven to be a worthy opponent, despite having gone well off the deep end. - Runner-up for this game has to be Mimi. Cute little diva girl, right? Oh, wait until you get to that level. Rumor has it that she's caused dozens of people to become arachnophobic. - Mustache Girl, A Hat in Time: Can you really call her a villain? At first, she seems like "some kid" until you get to know her. She has an amazing rebellious spirit, and her design really ties in to that. And to those people who thought she was just being petty? Well, uh, the DLC came out... with her backstory. It's impossible to see whether she's really the villain, or the hero that she thinks she is. - Jambastion Mages/Hyness, Kirby Star Allies: It's no secret that I love Kirby, but these four are amazing. Three blind worshippers - blind to the point where they literally got hypnotized by a priest of dark arts - and the Officiant of Doom make for a crazy group of believers. And even Francisca and Flamberge show a lot of personality in what little dialogue they've had so far! - Sectonia, Kirby Triple Deluxe: I've talked about nutty villains before, wait until you see this. A... bee that used to be her servant's best friend, turned insane all because of a mirror, before proceeding to destroy a land... all for beauty. She's chilling, malicious, and she has definitely reached that state of beauty she so yearns for... but at the cost of her sanity, then her only friend, then her life. She lost everything... all because of a mirror.
Damnnnn I've played an embarrassing amount of games in my time :') But I suppose the villains I liked the most were; Handsome Jack from Borderlands 2 Baron Praxis from Jak II: Renegade The Sorceress from Spyro 3: Year of the Dragon Red from Spyro: A Hero's Tail Ripper Roo from Crash Bandicoot Gleeman Vox from Ratchet: Deadlocked Clockwerk from Sly Cooper & The Thievius Raccoonus Reflux from Rayman 3: Hoodlum Havoc Anubis from Zone Of The Enders Jetstream Sam and Senator Armstrong from Metal Gear Rising: Revengeance Kaos from Skylanders series Moon Bear King from Puppeteer Frank Fontaine from Bioshock Zinyak from Saint's Row IV Dutch van der Linde from Red Dead Redemption series
Fou-Lu, breath of fire 4 you even get to play with him in certain chapters of the game! I have to find the gamesharq code to have him in your team the whole game one day...