X-Men: The X-Men have featured plenty of these throughout their run, among them one who was possibly the single greatest Trope Codifier, Cable.
Cable, of the New Mutants, X-Force, and the X-Men was a major influence in every example who came after. Tragic and mysterious past? Check. BFGs coming out the ass? Check. A "badass" look that used to be reserved for villains? Check. His first appearance was even in February 1990. Over time, though, he's been developed into a more heroic/complex character, somewhere between Messianic Archetype and A God Am I.
According to the rec.arts.comics.marvel.xbooks FAQ, Rob Liefeld originally designed him as a villain, but later reused the original design when he was asked to create a "New Leader". Not too long after, though, he returned to the original plan and created Stryfe, while still maintaining Cable in his position.
Cable's leadership was also a catalyst in giving the existing members of the New Mutants a 90's Anti-Hero look, even though many of them did not have the personality traits.
Not long after Cable's introduction, Liefeld followed up with Feral and Shatterstar, who were basically 90's Anti-Hero expies of Wolfsbane and Longshot respectively.
Bishop, another X-Man that followed the pattern of being a huge, muscled fellow with big guns in a Crapsack WorldBad Future.
Wolverine is perhaps the one other man who can contend with Cable's title as the Trope Codifier. While Wolverine predated the era, having been conceived in the 70's, Wolverine would come to possess many of the trademark qualities including an anti-authoritarian attitude, willingness to kill, and a gritty, dark backstory that defined many such characters. Especially during the 90's where his characterization he devolved into "stabby stabby stabby!"
Cyclops, of the X-Men, had his personality largely unchanged, but despite having been nicknamed "Slim" his whole life suddenly developed a chest that pro wrestlers would find intimidating. His personality has changed later though. During Grant Morrison's New X-Men and especially after, he became pretty much Nineties Anti-Hero despite the fact that it started in 2003.
There's an obscure X-Men character named "Random", who started out as a recurring character for the second incarnation of X-Factor and can turn his arm into a gun. In Generation Hope #15, Pixie calls him "Johnny '90s". What's generally forgotten in later appearances is that Random is a shapeshifter who was actually a 13-year-old kid when first introduced, and took the form of a muscular giant with gun-arms because it's what he thought a badass was supposed to look like.
Psylocke was turned into a 90's antihero in-universe. For most of her decades-long publication history, Betsy was demure and preferred to use her psychic powers to win fights rather than engaging physically. All that changed when she was body-swapped with the Japanese assassin Kwannon and gained her martial arts skills, cold-but-aggressive personality, overt sexuality (her previous modest costumes were replaced by a leotard and thong), and willingness to kill. Ninja!Psylocke became the 90's antiheroine, even though she had been around much longer and the new incarnation was a totally different character in all but name.
Venom. First there was the "black suit" Spider-Man, basically a textbook example of this trope before its time. This was caused by an alien Symbiote bonding to him, which he later removes. It then bonds to another man, Eddie Brock, becoming Venom, designed to be an Evil Counterpart of Spider-Man. That would have all been well and good, except Venom proved to be something of an Ensemble Dark Horse, and entered his peak of popularity during the peak of this very trope's popularity, and thus Venom was given his own comic and re-worked into one. Then they have Venom's symbiote give birth to a second one, which bonded with a Serial Killer to become Carnage, an evil(er) counterpart of Venom. This opened the floodgates at this point: Venom's symbiote gave birth to five more symbiotes, but all but one of them fused into a single one. The fusion bonded with a police officer to become another 90's anti-hero Hybrid. Meanwhile, Carnage's symbiote also gives birth, the resulting symbiote binding with another another police officer to become yet another anti-hero, Toxin. Since then, however, the original Venom symbiote has exchanged hands a few times and and its then-current host was a normal Anti-Hero. "Flash" Thompson even managed to give Venom the classic '90s Anti-Hero look, as he regularly used big guns along with the Venom powers, and the symbiote looked like a body armor suit when bonded with him. Venom himself moves on from this trope when the symbiote jumps back to Eddie; since at this point, Venom is now trying to become just a regular hero.
Kaine. Seriously, just look at him.◊ (At least he was salvaged in Spider-Girl.) And in the 2012 Scarlet Spider comic series written by Chris Yost, Kaine is now reluctantly (the reluctant part coming in with his regularly proclaimed ambition to move to Mexico and drink margaritas on the beach for the rest of his life. No one really believes him) trying to be more of a traditional super-hero and move away from this motif altogether, as part of an attempt to live up to his 'brother' Peter, who he considers to be generally a far better person, and to be an example to his Morality PetAracely, usually coming off more as a Knight in Sour Armour. On top of that, he is aware that he used to be an awful person. Moreover, he believes wholeheartedly that he still is, simply telling Aracely to leave it at the end of his solo series when the residents of Houston (including his girlfriend) freak out and reject him after his transformation intoa giant spider monster in order to destroy Shathra and save lives, and she tries Shaming the Mob.
Morbius. Edgy leather gimp suit, magical demonic powers, slaughtering bad guys by the dozen, less moping and more badass-itude and even more exaggerated 90's villains to fight with... Only aversion might be that the 90's comic made him more generic handsome.
The entire plot of Superior Spider-Man (2013) sees Doc Ock stealing Peter Parker's body and using it to become a darker, more "badass" version of Spidey. He even has a black and red costume that was originally designed by Alex Ross for the first movie (since Movie Superheroes Wear Black). The entire thing requires all of Spider-Man's friends and teammates somehow not realizing that Peter Parker has been replaced. But like Azrael was to Batman, it ends up being a deconstruction; as Doc Ock slowly loses control over the situation until he's forced to concede that Peter Parker is, in fact, the "superior" hero.
Spider-Girl has April Parker, that is simply a jerk version of main protagonist with the powers of Venom. She fits this trope perfectly, right to the point that a woman she once saved from bandits runs away, because she is more violent than they are. Oh, and she killed Tombstone, too.
One of Spider-Man's lesser villains, Cardiac, was one of these.
The second-tier Marvel superheroes Darkhawk and Sleepwalker, both of whom had their heyday in the early 1990s, are downplayed examples of this trope. While they have strange and bizarre appearances, neither one was especially dark in their tone, at least compared to titles like Spawn, or the other characters that exemplify the Nineties Anti-Hero.
Darkhawk was about a kid who followed in his policeman father's footsteps by fighting crime with the mysterious alien armor he had obtained, while simultaneously keeping his Nuclear Family from falling apart. At one point he finds a journal of his father's, the last entry stopping with him and his partner preparing to go in pursuit of a hit-and-run driver before seeking medical attention for his victim. Chris refers back to this several times to remind himself to take a harder edge, before discovering the journal had a stuck page, in which his father hesitates, calls an ambulance, and makes sure the old woman who was hit survives.
Sleepwalker was about an alien from another dimension that became trapped in a human's mind and manifested to fight crime while he was asleep, carrying on the similar role he had carried in his home world. Despite his scary appearance, Sleepy was very much a straight hero in terms of personality, adhering firmly to Thou Shalt Not Kill and several times giving up chances to return home in order to help others. There were, both in the letter columns of the old Sleepwalker comics and more recent web postings, positive responses from fans who liked the fact that Sleepwalker wasn't a violent antihero.
A strange example is Deathlok the Demolisher, who was created well over two decades before the heyday of the trope. Each of the various versions of Deathlok have very 90's Anti-Hero traits to them: he is always a dead man resurrected as a cyborg (cyborgs being common in 90's comics), and turned into an unliving cybernetic weapon that uses huge guns as its primary method of offense. Usually however the plot often involves Deathlok's unwillingness to succumb to his programming and kill wantonly, instead struggling to non-lethally dispatch his foes.
Rachel: You know what gives me strength? My loss. We're alike that way, I imagine. Admit it: nobody who's a stranger to that particular pain could ever be as driven as us. Matt:Never...*throws one of his sticks at a wall so hard behind herit plants in it*... Don't you ever say that to me again. That is a repellent statement. It is a vomitous insult to every cop — every fireman — every soldier alive who steps up to fight for those who can't! I am sorry for your loss! But if you genuinely believe that only the death of a loved one can motivate a human being to take up a cause... then get your pathetic, cynical ass out of my way so I can do my job!
Speaking of The Punisher, he definitely fits this trope when written by certain authors. He's vacillated between a somewhat reasonable vigilante fully willing to abide by other heroes no-killing rules during team-ups, to an frothing lunatic who'll murder jaywalkers (retconned into being due to drugs he was exposed to without his knowledge), to being a mass murderer who uses his family's deaths as a justification for the endless war he wages to sate his bloodlust. This third characterization is undoubtedly the essence of Frank in the MAX imprint.
Penance in the Marvel Universe, originally the happy-go-lucky character Speedball, is a strange version of this. After believing himself responsible for the death of 612 people in Civil War (2006), he designs a costume in dark colors designed to give himself constant pain with 612 spikes. This was intended seriously, but having happened long after the 1990s, is treated like a parody in most of his appearances outside Thunderbolts.
The Winter Soldier mega-arc by Ed Brubaker in Captain America subverts a lot of these tropes. When Cap's sidekick Bucky turned out to be Not Quite Dead after all, he was revived as a brainwashed assassin with a cyborg arm; it could have been really stupid, but it wasn't. Then, when Bucky took over as Captain America, he seemed poised to be a Grim and Gritty alternative to the more traditional model, with much made of him carrying a gun — however, Bucky almost never uses the gun, and in fact tries overcome his past and be a more traditional superhero.
Nightwatch from Marvel (as well as the Chase Lawlyer version of Manhunter from DC), both of whom were rather shameless rip-offs of Spawn.
Death's Head II is an amoral, almost unstoppable skull-faced cyborg with a hand that shapeshifts between claws, blades and guns, as required. His spin-off Superior SuccessorDeath Metal turns all of this up to eleven.
Die-Cut is an alien warrior who's back from the dead in a genetically engineered body with a huge blade grafted to one arm and a crazed mindset. The only subversion is that he values life and really doesn't like killing humans or other organic sentients. However, he also thinks all cyborgs and robots are abominations that must be destroyed, so...
, Rob Liefeld originally designed him as a villain, but later reused the original design when he was asked to create a "New Leader". Not too long after, though, he returned to the original plan and created Stryfe, while still maintaining Cable in his position..png){kind=small}
