The Atom has The Floronic Man, the Bug-Eyed Bandit, The Thinker, Dwarfstar, Lady Chronos, the Panther, Wizardo, the Man in the Ion Mask, Xotar, and of course, Chronos.
Batman is a standout example, both in terms of memorable villains and in terms of sheer size. Many individual members of the Bat-Family all have their own rogues galleries, too. Combine them all and you have one of the biggest rogues gallery in comics history, with new members being added all the time:
The most famous examples include The Jokernote an incredibly deranged man who looks like a clown obsessed with Batman himself,The Scarecrownote a psychologist dressed in a scarecrow costume who is obsessed with fear, Two-Facenote an attorney who became obsessed with duality after half his body was disfigured, Poison Ivynote a woman capable of controlling plants and an eco-terrorist, The Penguinnote a scion of a wealthy family who was born heavily disfigured; now a crime lord in Gotham City, The Riddlernote a criminal mastermind obsessed with proving his own genius by leaving difficult clues behind, Catwomannote a cat burglar who has an on-off relationship with Batman, Mr. Freeze,note a cryogenicist trapped in a cooling suit; he is seeking money to revive his frozen wife, Hugo Strangenote a scientist and psychologist also obsessed with Batman, being one of the few to have been able to deduce his true identity, Hushnote scion of a wealthy Gotham family who wants revenge on the Wayne family, Harley Quinnnote a former psychiatrist of Arkham Asylum who became infatuated with The Joker, Clayfacenote a series of characters who all have clay-like bodies that allow them to take on the appearances of other people and reshape their bodies at will, Killer Crocnote a man with a rare genetic deformity that gives him crocodile-like characteristics, Ra's al Ghulnote the seemingly immortal leader of an Ancient Conspiracy dedicated to steering society, and in one continuity is also Batman's mentor, Talia al Ghul, note Ra's loyal daughter who's often either a foe or Love Interest to Bruce, Deadshotnote a Professional Killer with almost supernatural aim, Banenote an exceptionally intelligent man who was raised in a prison and experimented on with a combat drug, Mad Hatternote a madman obsessed with Lewis Carroll's Alice in Wonderland, and Black Masknote a crime lord obsessed with masks; the mask he wears was fused with the skin of his head after a fire.. He's also got a bunch of lower-tier but still important villains like Man-Bat, Killer Moth, Firefly, the Ventriloquist and Scarface, Tweedledee and Tweedledum, the Great White Shark, Victor Zsasz, the Court of Owls, Professor Pyg, Maxie Zeus, Calendar Man, Solomon Grundy, Lock-Up, Talon, Lady Shiva, Anarky, Dr. Phosphorous, Ratcatcher and Cluemaster.
Depending on the continuity, poor Batman has had to deal with multiple rogues galleries. On the 1960s TV show, King Tut and Egghead were particularly troublesome. The animated series gave us the Clock King and its spinoff comic The Batman Adventures gave us, among others, the trio of Mastermind, The Professor, and Mr. Nice (although they were more in the Ineffectual Sympathetic Villain category, really). And Gotham adds Barbara Kean, Theo and Tabitha Galavan, Jerome and Jeremiah Valeska, and Fish Mooney to its Rogue roster, although they and the rest are more Jim Gordon's Gallery than Bruce Wayne's.
Batman's former sidekick Nightwing has his own gallery, including villains that have plagued him from his days with Batman and the Titans: Blockbuster, Torque, the Tarantula, Nite-Wing, Double Dare, Hellhound, Amygdala, Deathstroke, the Pierce Brothers. In a subversion, one of them is Shrike, an assassin Nightwing befriended while undercover receiving assassin's training. He thinks that he's Nightwing's worst foe; in reality, Nightwing doesn't even consider him a threat, on one occasion ignoring him and walking away while Shrike chased after him, trying (and failing) to hit him.
Deconstructed in Bates and Weisman's version of Captain Atom, in which Cap had a fictitious rogues' gallery that the military designed for him as part of his publicly-revealed false origin. Since that origin was his original, Silver AgeCharlton origin, his fake rogues' gallery, most notably Dr. Spectro, were drawn from his actual Charlton stories. On top of which, some of these fake villains later becamereal ones. Plus which, they, along with many of his other actual rogues, including, again, Dr. Spectro, as well as Major Force, The Ghost (at one time), and Wade Eiling, worked for the same secret military project he himself worked for. He also had "regular" rogues like Plastique, The Cambodian, and the Queen Bee.
Firestorm has a Rogues Gallery that could be charitably described as deficient. Not only are the vast majority laughably underpowered compared to the hero (who has to carry around an Idiot Ball the size of a house for them to be any threat to him whatsoever), but they seem to made up mostly of perverts or offensive stereotypes. This article covers several of the worst offenders. But at least there were both Killer Frosts, Typhoon, Brimstone, and Tokamak. None of whom were slouches in the power department.note The Killer Frosts are among the deadliest examples of ice powers in fiction, Typhoon is basically a sentient typhoon in humanoid form, Brimstone is an immensely powerful fire elemental created by the Big Bad of the entire DC Universe, and Tokamak has the same story-breaker powers as Firestorm.
Enemies peculiar to the Golden Age Flash Jay Garrick included the Turtle, the Thinker, the Fiddler, the Thorn, the Eel, Star Sapphire (an alien queen from another dimension and not to be confused with the similarly-named Green Lantern villain, though later revealed to be a former Zamaron queen), the Rival (Jay's own Reverse-Flash, who wore a darker version of Jay's costume with a mask), Rag Doll, The Shade, and Vandal Savage.
Barry Allen has an impressively large selection of enemies, the most recognizable of which include Captain Cold, the Trickster, Mirror Master, Captain Boomerang, Weather Wizard, The Shade, Pied Piper, Gorilla Grodd, Heat Wave, Golden Glider, the Top, Professor Zoom/Reverse-Flash, etc. They were also marked being a really unambitious bunch, considering they all have some incredibly powerful tech and the best use most can think of is simple robberies of local targets. It's implied that many are at least as unstable as Batman's. Most actually called themselves "The Rogues" and are unusually social for supervillains. Gorilla Grodd and the original Reverse Flash are not members of and actually hate the Rogues (the feeling is mutual — the fact that said villains are probably the most heinous of the Flash's foes is implied to play a large part in the mutual dislike). The Rogues, in turn, have shunned other members of the Flash's Rogues Gallery, such as Abra Kadabra and the Rainbow Raider/s, though they will tolerate them when something big comes up (like Captain Boomerang's funeral) or when their goals coincide.
On the flip-side however, the Rogues have occasionally undergone a Darker and Edgier transformation to basically became Central City's version of the Mafia. While their gimmicks were still silly, they were unrepentant killers who were considered very dangerous.
Depending on when the comics were printed, some of Wally's Rogues were sometimes depicted as being Punch Clock Villains who were actually almost friendswith the Flash. Notably, scenes like this◊ actually happened in the comic, not just on the cover (that one happened because the Trickster sent Wally an invitation to a Rogues party as a joke - Wally had a date and no better ideas, so he decided to take him up on the invite. All involved find themselves having a surprisingly good time). Most prominently, the Pied Piper made a Heel–Face Turn and became genuinely close friends with Wally.
Bart Allen's tenure as the fourth Flash wasn't really long enough to build up a separate roster but, in addition to fighting Barry Allen/Wally West villains, he has Griffin, Superboy-Prime and even gains an arch-enemy of his own, Inertia.
Green Arrow: The titular Emerald Archer has his own gallery of rogues, some of whom are archers like himself, and many of whom tend to be professional assassins. These include Merlyn, Count Vertigo, Clock King, Constantine Drakon, Brick, Cupid, China White, Red Dart, Hatchet, Silver Monkey, Shado, Camorouge, and Onomatopoeia. Occasionally Oliver will clash with Deadshot, despite the two having no real animosity with each other, and with Deathstroke, who definitely carries a grudge against Oliver for stabbing him in his (already-blind) eye. Several of these would later show up as antagonists in Arrow (see below).
Green Lantern: Each Green Lantern to headline their own series has had a collection of recurring foes, though they rarely if ever have teamed up collectively.
Alan Scott: Vandal Savage (arguably his archnemesis), Solomon Grundy, the Sportsman, the Icicle, the Gambler, the Harlequin (who actually only became a villain in the first place to date, and, subsequently, marry Alan) and the Thorn (the mother of his two children).
Hal Jordan: Sinestro (definitely his archnemesis), the Manhunters, Kanjar Ro (a Rogues' Gallery Transplant - he was originally a foe of Hawkman), Atrocitus, Hector Hammond, Star Sapphire (Hal's sometimes-girlfriend), Dr. Polaris, the Tattooed Man, Evil Star, Black Hand, Goldface (another Heel–Face Turn), Sonar, and the Shark.
Kyle Rayner: Major Force (on loan from Captain Atom and not really his archnemesis, but he's loomed large in Kyle's life anyway, thanks largely to what he did to his first girlfriend), Oblivion, Grayven, Effigy, Alex Nero, Fatality, Sonar II, Amon Sur and acquired Brainwave JR, Dr. Light, Dr. Polaris and Hal Jordan as Parallax. Kyle, in an issue of his comic, bemoans the fact that he has a lousy Rogues Gallery, compared to his friend Wally West (The Flash).
As of Green Lantern: Rebirth and the subsequent relaunch of the franchise, Hal and Kyle's galleries have more or less merged into a collective Rogues Gallery for the entire Green Lantern Corps, with the additions of Parallax, Mongul, Cyborg-Superman, Superboy-Prime, Krona, and the Sinestro Corps.
Furthermore, the GL Corps now have their own rival factions, including the Red Lanterns, Black Lanterns, Agent Orange, and the aforementioned Sinestro Corps. The Star Sapphire name is now applied to a corps as well, although they don't have any designs towards antagonizing the Green Lanterns.
Hawkman and the rest of the Hawk-Family have had a number of enemies ranging from villainous fellow aliens and non-powered human criminals to meta-humans and even figures from ancient mythology, to include the likes of Byth Rok, Fadeaway Man, Gentleman Ghost, I.Q., Lion-Mane, the Manhawks, Matter Master, the Monocle, Lasso, Hath-Set, Headhunter, Hummingbird, Count Viper, Vandal Savage, and the Shadow-Thief, who's also their Arch-Enemy.
Even though her series is only 38 issues long, Kate Spencer, the Manhunter, has quite an impressive rogues gallery. Sweeney Todd, Copperhead, the Monocle, Phobia, Dr. Moon, Everyman, and Vesetech.
The Shazam! Captain Marvel: the Rogues Gallery includes Dr. Sivana (and all four of his children), Mr. Mind, Black Adam, Mr. Atom, Ibac the Invincible, Sabbac, Oggar, King Kull, the crocodile-gangsters of Planet Punkus, etc. Most (save Black Adam) haven't appeared much lately, but they tend to congregate as the Monster Society of Evil.
The Monster Society has the distinction of being the first recurring villain team in comics. So it was Captain Marvel's gallery who first came up with the idea of teaming up to destroy the hero (a tactic which proved about as successful as it usually does.)
The only unrepentantly evil members of the Sivana Family are Dr. Thaddeus Sivana, Georgia, and Sivana Jr. Magnificus and Beautia both pulled Heel Face Turns and became at the very least Law-Abiding Citizens who are mostly embarrassed by their family, if not outright allies of the Marvel Family.
To be fair, Darkseid and other elements of the Fourth World were introduced in Jack Kirby's Jimmy Olsen comics, so they were, by extension, always a part of the Superman Mythos. And, in any case, their storylines were awesome. It should also be noted that Darkseid and his minions had already been introduced and had been recurring archenemies for Superman in the comics for several years before Superman: The Animated Series was even produced and aired.
Supergirl has her own gallery, including Mad Scientist and body-swapper Lesla-Lar, Kryptonian criminal Black Flame, sword-wielding Amazon Nightflame, Satan Girl (name shared by three vastly different enemies), reality-warper Nazi Blackstarr, super-powered Darkseid minion Powerboy, mass-murderer bounty-hunter Lobo, Metallo expy and genocidal thug Reactron (who killed post-Crisis Supergirl's parents and blew New Krypton up), corrupt businessman Simon Tycho, Super-Soldier Reign and the remainder world-killers -biological super-weapons-, Kryptonian werewolf Lar-On, Cyborg-Superman, and many more.
In addition to their individual enemies, the Justice League of America had a handful of villains that regularly fought them as a team: Amazo, Despero, Starro the Conqueror, Kanjar Ro, Starbreaker, The Shaggy Man (later known as the General), The Queen Bee, and Prometheus, to name but a few. Two of the most famous villain teams are the Injustice League and the Secret Society of Supervillains.
The Justice Society of America's Rogues Gallery is made up mostly of the surviving foes of their individual members from back in The Golden Age of Comic Books, as well as said foes' legacies and a few add-ons from more recent years. These include but are not limited to: Vandal Savage, the Wizard, and the Ultra-Humanite (more or less collectively the team's archfoes), plus Per Degaton, Wotan, Solomon Grundy, the Rival, the Tigress, Shiv, the Gentleman Ghost, Johnny Sorrow, Roulette, Icicle II, the Thinker, Killer Wasp, Rag Doll, and on-again-off-again Anti-HeroBlack Adam.
Both the League and the Society occasionally fall foul of various terrorist groups (Kobra, the Illuminati) and shadowy government organizations (The D.E.O., S.H.A.D.E., The Agency, Checkmate).
The Legion of Super-Heroes has loads and loads of recurring enemies, including at least three teams of villains:
The Fatal Five: Tharok, Manos, Validus, Emerald Empress, and the Persuader (plus, on one occasion, Mordecai standing in for Validus).
The Legion of Super-Villains: Lightning Lord, Saturn Queen, Cosmic King, Chameleon Chief, Esper Lass, Hunter, Magno Lad, Micro Lad, Nemesis Kid, Ol-Vir, Radiation Roy, Ron-Karr, Spider Girl, Sun Emperor, Tyr, and Zymyr.
The Justice League of Earth: Earth-Man, Storm Boy, Golden Boy, Tusker, Eyeful Ethel, and Radiation Roy and Spider Girl from the LSV.
And numerous unaffiliated villains: Mordru, the Time Trapper, Computo, Universo, the Dark Circle, Leland McCauley, Imperiex, Evillo, Grimbor the Chainsman, and so on and so forth.
Static, despite having a relatively short history, has built up a very respectable rogues gallery over the years. This includes main-stays like Hotstreak, Ebon, Rubberband Man, Holocaust, Talon, Shiv, Carmen Dilo, Kangor, Onyx, Puff, Ferret, and Aquamaria, not to mention the loads of one-off or lesser prominent foes the rebirth of cool has faced off against. Being the defender of Dakota City, Static has also faced off against entire entire groups, from small criminal enterprises to large organizations, such as the Ruff Pack, Sons of Odin, Meta-Breed, Meta-Men, Alva Corporation, and well, the police.