The G-Man from the Half-Life franchise definitely qualifies. Always showing up in the life of Dr. Gordon Freeman to push him once again into center stage as a shining protagonist... If Gordon is always the unquestionable hero in these events, why do the "deals" he offers Gordon feel so Faustian? And the G-Man has shown us glimpses of godlike power - so what's the real game he's playing here? One thing's for sure - observing the G-Man's strange powers, and even just listening to his oddly inflected voice. Whatever is behind those enigmatic eyes...is certainly far from human...
Far Cry 3: Vaas Montenegro. Thanks to Michael Mando's hammy yet terrifying performance, the iconicity of Vaas solidified him for instant fan approval, and continues to do so now. And this is only complementing his badassery, his dark sense of humor, his sophisticated nature, and his incredibly iconic definition of insanity. You know that a villain is really compelling when many fans consider him a far better character than the protagonist himself. It certainly helps that he has more charm than Buck and Hoyt.
Subverted with Niko Bellic from Grand Theft Auto IV. While he is a man who wants to get away from violence and crime, more than one NPC will be surprised by how effective he is as a Professional Killer.
Grand Theft Auto V carries on the tradition. In particular, Trevor Philips is far and away the most psychotic of the three protagonists. He's also the most badass.
The Xenomorph in Alien: Isolation is simultaneously terrifying and fascinating, both due to its unpredictability and remarkable adapting AI. Throughout the story, it puts the player through multiple, highly tense cat-and-mouse games, that will make the player fear turning every corner. In the minds of many, it successfully made the Alien genuinely scary again.
Looking back at Guilty Gear, many people were turned off by Ky Kiske because he's too much of a goody two shoes. Then, in BlazBlue, he's given an Expy in form of Jin Kisaragi, a twisted, erratic Jerkass whose unwholesome personality was nonetheless well-met by many fans, though he does become a case of "Morally Ambiguous is Cool" post-CS.
There is the matter of Hazama, a.k.a. Yuuki Terumi, who's taken the role of the Big Bad of the series. He's an arrogant Troll who's even more abrasive and mean-spirited than Jin and has more or less fucked up the lives of everyone in the series, most of all, Noel, when he transforms her into Mu-12. Fans love him because he's funny, handsome, and a cool dresser.
Although over time, people somehow got sick of Terumi being constantly pushed to attention and looking too invincible nearing Boring Invincible Villain status. On the other hand, this title now goes into his partner Relius Clover, who's not as pushed to attention, but remains a Large Ham, composed, a cool dresser, rugged, and just as depraved as Hazama (or even more).
However Terumi becoming a separate playable character form Hazama made fans love him again, mostly due to the fact that he took Hazama's personality and threw any and all restraints aside. And then the fourth game boosted it even further when he kills the coolest good guy, Hakumen, and then reveals he's actually a literal god.
Nine and Izanami as of the fourth game got into this.
Especially in Red Alert, the evil is served with a generous side of Large Ham. The Soviets are supposed to be the "bad guy" faction, but they have psychic troopers, tesla coils, the best tanks in the games, Kirov airships, spider-like terror drones, mind-controlled giant squid, battle-bears, and nuclear missiles to spare!
Yuri's faction Red Alert 2, while its overpowered status has its usage in multiplayer frowned on, fans agree that its gimmicks make it fun to play as and many fans were disappointed that it didn't get its own campaign, so many of the mods to the game, in addition to balancing the faction, focus on giving it one.
Starting in Tiberian Sun, Nod had much cooler outfits than GDI, and in Tiberium Wars, they had cooler looking vehicles. This is somewhat offset by the fact that Nod has a tendency to favor looks over practicality. GDI's ground vehicles tend to be better, and their soldiers actually look like soldiers, while Nod's look like a bunch of, abeit cool looking, KKK rejects.
In Demonheart, all of the major characters and romance options are evil to some extent, and the good seeming characters are quick to lose the protagonist's respect, turn out even worse than the cool bad guys, or meet an untimely death.
Used quite a bit the Devil May Cry series. Dante's enemies (primarily his Evil Counterpart, his brother Vergil) are pretty darn cool, but Dante still generally mops the floor with them with style.
If this video is of any guideline, Baal from Diablo 2 counts.
Through not exactly a villain at the moment(but perhaps will be a antagonist an X-Pack), the Knight Templar Angel Imperius from Diablo III seems to be heading in this direction given his badass armor design and the short but badass fight between him and Diablo at the beginning of Act IV.
Disgaea characters believe in this trope, but it ends being subverted when an actual villain appears as they also turn out to be too much of a Jerkass to apply to this trope.
Practically the point of Dungeon Keeper, where you are the Dark Lord who builds his eldritch underground kingdom and throws adventuring heroes in torture chambers. Remember: Evil is Good.
Jack of Blades from Fable may murder your mother and blind your sister among other things. However, being one of the few well-voiced characters in the game, the first Big Bad in the series, and just generally an all around badass Humanoid Abomination/Eldritch Abomination, he earns this status. He easily ranks as the best villain in the series.
Conversely, the new Brotherhood of Steel could be seen as this. On one hand, they have genocidal tendencies towards Synths, ghouls, super mutants and other non-humans with Nazi-like fanaticism, but on the other hand, most of these are Always Chaotic Evil monsters anyway (it's the Brotherhood's refusal to acknowledge a few aren't that makes it a Kick the Dog from them). Whether the Brotherhood of Steel qualify as evil is arguable, but what isn't is that they're awesome. Knights clad in T-60 power armour, fleets of Vertibirds, a Cool Airship, and they've even rebuilt Liberty Prime!
Kotomine in Fate/stay night...well, he's cool enough that the fact he has a mullet ceases to matter. Possibly helped along by every scene contrasting him to Shirou. The other Big Bad, Zouken, is not cool. Or likable. Or, well, tolerable. You just kind of want him to hurry up and die already. Helped by the fact that Kotomine really knows how to talk; it's hard to be bored of his often long speeches. Most of his speeches have very little to do with him being evil or evil in general.
Pick a Final Fantasy game, go ahead, pick one. To recount some of the more famous examples:
Ardyn Izunia: While there's a considerable Broken Base regarding changes made to the fifteenth game's story, the one thing fans near unanimously approve of is making Ardyn Iznuia the new Big Bad. He's the enigmatic yet stylish chancellor of Niflheim, has a mysterious backstory and strange powers, drives a Cool Car, and constantly speaks in a tone of voice which is somehow both oily and suave at the same time. He gets the best lines in the game, makes no pretext in hiding how evil he is, and is a Magnificent Bastard whose schemes tend to go off without a hitch. He's also a man turned into an immortal Humanoid Abomination from all the daemons he's absorbed into himself, which just helps make him Creepy Awesome as well. As the cherry on top of his cake of evil, he also stars front and center in the game's final DLC campaign, in which players take control of him and raise high hell!
Kratos from God of War is an excellent example, as his very anti-heroic tendencies make him a more interesting character. He's a complete badass. though in a subversion, some fans fond his progressively worse actions in the sequels made him hard to root for.
Ares, to a certain extent, though he is not so cool as Kratos due to being such a despicable character. He has coolhair, that seem to be made of fire. And his armor?? Man, best armor in the franchise!
Zeus in the sequels, probably the only one of the villains besides Ares to get much of following since A, the major antagonists besides him and Ares don't have much personality, or even screen time, and B, he's the king of the gods and shows why since he fights barehanded in a series where nearly everyone else uses some sort of weapon, and defeats a titan while human sized.
The game's version of Brainiac, thanks to excellent voice-work is one of the scariest takes on the character. The fact that it's a perfect fusion of his original Silver Age appearance and shtick (complete with impenetrable shields) and the DCAU (the "collect all knowledge and destroy the prototype" plan) makes it a perfect Adaptation Distillation.
This Scarecrow gets a large amount of this from fans for being essentially Freddy Krueger in the DC Universe. It helps that he is played wonderfully by Robert Englund who gives him some great biting dialogue and his visuals are phenomenal and Creepy Awesome.
Par the course for the character, Darkseid also got this treatment specially for his awesome booming voice which is accompanied by no shortage of signature boasts and his cool Super Move.
The Helghast of Killzone, with their Jin-Roh inspired battle armor (the Custom Uniforms of which are extra-awesome◊), sympathetic back story, and a leader that gloriously feasts on ham. Every time a sequel is announced, the fanbase hopes they'll finally be able to play as them in single-player mode...and then they get stuck playing the painfully generic loud-mouthed American soldier guys of the ISA again, killing legions of people much cooler-looking than you.
Riku also qualified when he appeared in the first game.
It is primarily for this reason that Knights of the Old Republic and similar games have an evil option. KOTOR is further helped in this regard, since Star Wars villains are generally among the most badass characters in all of fiction.
This is acknowledged in the second game, where the opening screen shows one of the various Sith Lords of the game. Go bad enough, and your character will replace them after you complete the game.
The King of KOTOR Kool himself - the psychotic, homicidal HK-47 assassin droid. "Definition: 'Love' is making a shot to the knees of a target 120 kilometers away using an Aratech sniper rifle with a tri-light scope." He is far and away the single most beloved character by the meatbags playing the games, even though he's regarded as among the least useful in gameplay.
Both KOTOR games actually provide especially good foundations for this. In the first game, you're playing an amnesic Sith Lord, and if you decide to reclaim your former glory, characters will acknowledge you as such. And KOTOR II just takes it Up to Eleven. This time, you aren't technically on a mission to be the hero, so it's not even expected of you. In this game, you get to wear a black Badass Longcoat, teach your companions the way of the Dark Side, cut your way through small armies like a knife through butter, take out entire ambush teams of mercenaries with a single Force Storm, curbstompJedi Masters in a duel, steal their techniques, then suck up their power for yourself...and that's all before you get Force Crush, against which there is no defense! The Light Side path may have more plot exposition, but the Dark Side one is definitely the cooler one.
Star Wars: The Old Republic also has a Dark Side path for this reason, even for the Republic side. Yes, you can pretty much do a Renegade Shepard run as a Republic Trooper, be an underworld thug as a Smuggler, and go full Anakin Skywalker ExpyKnight Templar on the Jedi paths. If you do a dark side Imperial run, you're even more of a puppy-kicking, manipulative, brutal monster...but wow, you can certainly look cool doing it. And even if you go light side Imperial, you can still benefit from being a badass Sith Lord/secret agent/assassin for hire while still maintaining your real-life moral compass.
It's lampshaded in-game by Kira (a Jedi Knight companion) : "Have you seen what the Sith are wearing ? It's like every fashion designer in the galaxy went over to the dark side".
Also from Star Wars, Star Wars: Battlefront II has you playing as the 501st Legion in the "Rise of the Empire" story mode. Needless to say, after the Evil Empire rises and the 501st becomes evil, they're still awesome.
Big BadUltron-Sigma has been well-received as a very cool and threatening villain with one of the best designs and voices in the game. Inflicting an utter Curb-Stomp Battle on the heroes at the start of the story and having a flashy fighting style does help his badass credentials quite a bit.
Thanos — for his epic fight against Ultron-Sigma, managing to break the Reality Stone with his bare hands, and stealing Ryu's Satsui no Hado to make Lady Death pay for treating him like an Unwitting Pawn... all while speaking in the smooth Badass Baritone of Isaac C. Singleton Jr. and generally being, well, Thanos. Even despite him being shackled early on.
Jedah. He's generally considered to be one of the best-produced characters on the roster, thanks to his Darkstalkers movelist translating well, an awesome trance remix of his old theme, and a Large Ham performance thanks to David Kaye.
As evil as they are, you have to admit the Reapers from Mass Effect are pretty cool. They're unfathomably advanced squid-shaped spaceships with apparently no desire beyond killing everyone every few thousand years because, hey, why not?
Daveybird from the Randle Sim Racing mods is the host and organizer of the RSRA league, and can be pretty corrupt in his officiating and driving style, and is a villain for those storylines. He clearly cheats, and imposes rules that slow his competitors down, all so he can take the glory. But he's still adored by fans, and he loves that role as well as his heroic side.
Ristill might be the weakest of the Ancestors, but she proves to be a clever schemer and a Mad Scientist who comes up with ways to make up for the power discrepancy. She also has a past-paced boss theme that really highlights how frantically difficult she is after she uses Maxwell to gain an infinite supply of mana. Even Khaos notes that her ability to create existence from nothing is a potential Story-Breaker Power, which is proven true when her ability renders his Combat Clairvoyance useless.
Khaos is a Badass Bookworm who managed to discover how to control time and space, among other magical concepts that he studies. He's also the most powerful of the three because he knows how to apply his vast knowledge to combat, as shown when he uses time-based spells to give himself extra turns and predict the future. Better yet, the latter spell replaces the ordinary battlefield with a purple space, magic circle platform, and spinning gears in the background. The evil part is downplayed because he used to be the Ancestors' Token Good Teammate and is only the main antagonist because he wants to control time and space to bring his lover back.
Admit it: even after you find out that his cluelessness and uselessness was a disguise, you can't help but love Adachi Tohru from Persona 4. The reveal that he was the Killer all along actually added to his appeal as a character. His tendency to switch between Laughably Evil and delicious evilness makes him both entertaining yet intimidating in the eyes of the fanbase.
The Shadow Selves in 4 and Persona 5 are also pretty freaking cool, especially in their giant monster forms.
Tyranitar and Hydreigon, a Godzilla/Tyrannosaurus Rex and a King Ghidorah/Hydra Pokémon respectively. Both of them are extremely savage and destructive, are Dark-types who use actualdarkness powers as compared to most other Dark types, and their BST of 600 makes them comparable to some legendaries in terms of power. (Unsurprisingly, they're both in the OU tier.)
By far the most popular "shiny" Pokémon coloration belongs to Charizard, already an enormous Ensemble Dark Horse. In its shiny form, it gets an evil-looking black color scheme with blood-red wings and sinister red eyes (this form was actually depicted as a Darkness-type in the TCG in one card, and the card is one of the most sought-after and ridiculously overpriced cards today).
Unlike Reshiram and Zekrom, Kyurem is a truly evil (or at least corrupt) Pokémon by nature that eats humans. And it's a giant icedragon that can absorb Reshiram or Zekrom to switch forms and become more powerful.
Genesect, an apex insect predator from the Paleozoic period, can be interpreted as an evil(er) counterpart of Mewtwo; being revived by Team Plasma and cybernetically enhanced (such as attaching a laser cannon to it) to be the strongest Pokémon ever.
Yveltal, the gigantic bird-like Destruction Pokémon, screams this trope.
Incineroar, the fully-evolved Fire-type starter from Pokémon Sun and Moon. It's an extremely manly Fire/Dark bipedal tiger with the personality of a heel wrestler, complete with a championship belt made of fire. While it's a Base-Breaking Character (quite fittingly for its status as a heel), it has fans that love it a lot, many of which are in the Bara community. This also applies in-universe, as its "bad guy" act makes it popular with children.
Necrozma is an all-black prism creature that steals light from worlds and, like Mewtwo before it, is abnormally cruel and savage in battle, laying waste to areas with lasers and ripping foes apart with its claws. It even has a One-Winged Angel state with higher stats than Arceus. And the kicker? Unlike all the other Pokémon examples, it's the Big Bad of a mainline game, where it openly has an agenda of its own with no Trainer or mastermind pulling the strings.
A lot of the evil organizations such as Team Rocket can be this with their stylish uniforms, cool hideouts, and intimidating Pokémon teams. More specific members of the teams who count are :
From Pokémon X and Y we have Lysandre for his very ravishing appearance, fitting for being a boss of Team Flare, a team whose goal is to attempt to make the world more beautiful by comiting genocide on humans and Pokémon alike.
Saints Row: Every chapter ends in an Eviler Than ThouCoup de Grâce. Almost everyone kisses the Protagonist's ass by complimenting his/her murderous psychosis. Arguably the coolest character in the series so far is unrepentant mass murderer Johnny Gat.
The reason Dr. Eggman is so popular is because of this trope. Seriously, he can make damn near whatever type of machine he wants for any situation and his various evil lairs tend to be among the best levels in the series, in addition to his various boss fights. His Affably EvilLarge Ham tendencies also play a large role, in that despite being a villain, he is such a jovial and over the top guy that you can't help but love his antics. You can only imagine how elated fans were when Sega finally stopped shafting him in favor of whatever Monster of the Week he had unleashed and finally let him shine as a villain.
Eggman himself seems to be a believer of this trope. In Sonic Adventure 2, if you choose Eggman's voice for the menus and go to the Chao Garden in Stage Select, instead of saying "select your character" like nearly every other voice option, he says "heroes are wimpy".
This trope may be partially the reason why Shadow started off as such an Ensemble Dark Horse as he has had nowhere near the good reception ever since his transition to Anti-Hero.
Nightmare in the Soul Series. His armor is damn cool, he carries a BFS as big as he is.
Gig from Soul Nomad & the World Eaters. He comes off as a threatening badass even though he's a Sealed Evil in a Can most of the game, along with having by far the funniest moments in it, though in an odd case of this trope he's on the hero's side.
Bowser, despite his Villain Decay and penchant for competitive sports over the years, is still a giant, spiky, fire-breathing turtle-dragon, and winning a one-on-one fight with him as a pudgy plumber will always be satisfying - and yet, he's still a powerful menace when he needs to be, especially in the main Mario platformers. Mario & Luigi: Bowser's Inside Story seems to play to this, where the big bad spiky dude is the main character (even if he ultimately has to save the Mushroom Kingdom) and, rather than being merely a comedic Butt-Monkey, he's shown as a Hot-Blooded badass when he needs to be, and still gets plenty of hilarious scenes. Subsequent Mario & Luigi installments run with this trope and depict Bowser as a much smarter and more menacing villain than in previous RPG's, all while keeping him as the Laughably EvilBoisterous Bruiser fans know and love. This trope was more-or-less acknowledged in the E3 trailer for Mario Party 10, which features a "Bowser Party" mode where one player controls Bowser and gets to wreak havoc on other players.
Wario, to the extent where he even got his own spinoff series. A greedy badass treasure hunter who despite his size and pudgy shape pummels enemies to oblivion with his bare hands, is immortal (at least in Wario Land II and 3) and actually uses his immortality to his advantage by doing stuff like setting himself on fire to burn enemies and destroy certain blocks, and happens to own a minigame company.
Fawful. Dimentio. Pretty much every villain in the franchise, to be honest. Cool technology and weapons? Check. Best lines in the series (especially Fawful)? Check. Look awesome? Also check. There's a reason many of the other bad guys end up being the Ensemble Dark Horse.
Thing Thing: Project 154 may be a sociopathic mass murderer, but he is easily one of the most badass characters in flash gaming.
All of the most popular factions in Total War: Warhammer are the evil ones. You have the batshit Crazy Is Cool Greenskins who live for a good fight against anyone, you have the sinister and blood and power-hungry Vampire Counts and their armies of undead puppets and horrifying monsters, you have the clad-in-black armour and extremely badass Warriors of Chaos, and you have the insane, braying Beastmen who want nothing less than the complete destruction of all civilisation. The absolute king of this trope however is Norsca: imagine a faction of hardass, seven-foot-tall, daemon-worshipping vikings with an army built around maximum killing power, and an array of monstrous creatures that rival the Vampires. You can even usurp Archaeon as the Everchosen and pledge yourself to one of the four Chaos Gods to gain a bunch of special benefits. Norsca is by far the most popular faction in the game, and all the better because it is effectively an entire officially sanctioned homebrew faction created for the game, and the whole faction is filled to the brim with obscure elements of the setting's lore.