Agent 327: Hendrik I Jzerbroot's most dangerous opponent is Boris Kloris.
Asterix: Julius Caesar would be this, even though there's a mutual respect between the Gauls and Caesar. Caesar is often seen as a Voice of Reason and above the pettiness of many of the prefects.
Astro City: Samaritan has Infidel, who have both traveled through time to change history and thwart each others' schemes. They give up the feud once they realize that neither of them will ever be able to destroy the other, even if the Universe itself is destroyed.
Atomic Robo has the Nazi Baron Heinrich von Helsingard. Dr. Dinosaur may also qualify for Robo in modern times.
Thomas Edison for Nikola Tesla and, by extension, Robo.
Majestic 13 for Tesladyne...and again, by extension, Robo, but also former agent and full-time Memetic Badass Jenkins this time.
In their fictional universe the characters from the two British ComicsThe Beano and The Dandy are arch enemies with frequent jokes but at the other's expense and infrequent raids between the comics. This arch enemy rivalry has died down quite alot since The Dandy's revamp. Also characters from within the two comics have their own arch enemies as well. Dennis the Menace (UK) has Walter the Softy, Roger the Dodger has Cruncher Kerr The Bash Street Kids had the Blob Street Kids, the Three Bears had Hank and Grizzly Gus (another more evil looking bear who hasnt been in the strip for years) and Desperate Dan had either Cactusman or Dangerous Dan McGroo.
This arch-enemy comic rivalry was taken further in the Fleetway comic Whizzer and Chips which was one comic which was made up of two comics and these two comics and their characters were archenemies with even more frequent 'raids' in the two comics than with the Beano and Dandy.
The Crow has Top Dollar, the man who arranged the murder of Eric Draven and his girlfriend.
De Kiekeboes: Balthazar is the most recurring antagonist in the series, though generally considered to be a Harmless Villain. Far more dangerous are Timothea Triangl- a James Bond type villain who underwent a sex change- and Dédé La Canaille, a criminal who wants to murder Kiekeboe for putting him into jail.
Scrooge McDuck has several different enemies competing for the title. He often combats the Beagle Boys, though Blackheart Beagle, the oldest member and their founder, is the only one whom Scrooge has a personal vendetta with. His business rivals Flintheart Glomgold and John Rockerduck sometimes function as his own personal arch enemy(ies) too, given their status as Evil Counterparts of Scrooge. However, his most dangerous opponent is the witch Magica Despell, who threatens to steal his lucky dime and melt it in the Vesuvius volcano. One could also add Arpin Lusene, a Gentleman Thief who holds the distinction of being Scrooge's only Worthy Opponent.
Donald Duck considers both Gladstone Gander and Neighbour Jones his personal arch enemies, though these are of the sitcom variety. He does have an extensive Rogues Gallery in Paperinik New Adventures, but no single bad guy has managed to stand out as his definitive arch-enemy.
Mickey Mouse as seen in more recent Mickey Mouse Comic Universe stories has his own kind of dynamic with his two arch enemies Pete and the Phantom Blot. Mickey is typically more or less an Amateur Sleuth, naturally opposed to both of them as professional criminals. Pete is generally shown as a more crude but very experienced and enterprising criminal, whereas the Blot is a shadowy criminal mastermind. Pete is not completely evil and has been shown with a kind of affection towards Mickey as an opponent and is more prone to end up in an Enemy Mine situation with him, whereas the Blot is closer to being simply sociopathic. The two can even get contrasted in the same story, with Pete more human and the Blot more effortlessly smooth and evil. It's still Depending on the Writer.
Jommeke: Jommeke and his friends are often confronted by Anatool, the servant nobody can trust. However, he is somewhat of a Harmless Villain, seeing that Jommeke and his friends can easily thwart his evil schemes. De Koningin van Onderland ("The Queen of Onderland") on the other hand doesn't appear that much in Jommeke's stories, but when she does she is generally considered to be his most frightening and dangerous opponent.
Lucky Luke: Lucky Luke most often faces off against the Daltons. About half of the albums are about the Daltons and the rest about everyone else. Billy the Kid is the second most recurring villain and he still doesn't come close to their approaching Villain Protagonist status.
The Mad Hatter: The Gargoyle, a criminal resurrected as a Beast Man, was clearly supposed to be this for the Mad Hatter, due to the implication that he'll return, but he debuted in the final issue of the comic, so he didn't get the chance to full come into his evil.
One volume of Powers deconstructs the usual comic treatment of archenemies. It shows what were essentially the world's first superhero and supervillain. The two are immortal and have existed since humanity was still diverging from the ape, and have had a grudge just as long. When they meet for the last time in the present day, the hero, (who has a case of The Fog of Ages) demands to know why he and the villain have been fighting so long. The villain, whose memory is not impaired like the hero's, admits that he can no longer even remember what originally sparked their feud.
The Phantom: The Phantom is traditionally opposed by the current leader of the Singh Brotherhood; the 21st Phantom first battles Dogai Singh, and later, his daughter Sandal Singh. Other notable enemies include the mercenary Gold Hand and the evil President Lubanga.
Planetary and the Four, especially their respective leaders, Elijah Snow and Randall Dowling.
Jesse Custer in Preacher has Herr Starr, the Saint of Killers, and God. Yes, theGod.
Quick and Flupke: Quick and Flupke are often confronted by Agent 15. Seeing that the two boys are brats your mileage may vary whether Agent 15 is actually the hero of the series or not.
In "The Fires of Pharos", Commander Kaaj swears a blood debt against Captain Pike for destroying the Pharos siteworld. In "The Flat, Gold Forever", he lures Captain Pike away from the Enterprise with a Forged Message and attempts to kill him so that honor can be satisfied. When he later sees Pike on the Temazi homeworld in "Thanatos", he cannot contain himself. He attacks Pike in the Temazi shrine, thereby blowing both of their covers.
In the Alternate Timeline story arc "Futures", General Chang has seemingly taken Kaaj's place as Captain Pike's Klingon adversary. In "Now and Then, Part Four", he even compares his conflicts with Chang to "the bad old days with Kaaj."
Strontium Dog: Johnny Alpha has his father, Nelson Bunker Kreelman, a racist politician who abused and ultimately locked his own son up for his mutation, and leads a Nazi-like anti-mutant movement.
The Shredder to the Teenage Mutant Ninja Turtles and their mentor Master Splinter. Shredder goes down pretty early in the original comics. However, the first issue clearly shows the backstory Splinter and Shredder have, that Splinter and the Turtles owe their origins to Shredder, and that Splinter trained the Turtles for the sole purpose of killing Shredder to avenge Hamato Yoshi. Regardless of how long Shredder was around for, he's still their archnemesis.
The archenemy dynamic is played interestingly in the story. After Shredder was killed, the Turtles never really had another central enemy. A few issues show that the Turtles aren't really sure what to do with themselves with Shredder gone. In fact, in the City At War arc that capped off the original series, Leonardo argues that killing Shredder was more Splinter's goal than theirs.
Tomboy (Sterling): Despite being a One-Shot Character, it's heavily implied the Lard Vinsion, crime boss and Big Bad of Captain Flash #3, has tangled with Tomboy many times before, an honour no other villain receives.
Tom Poes: Bul Super and Hiep Hieper. Even though Joachim Sickbock and Hocus P. Pas are far more dangerous.
The Wasp (Lev Gleason): The Professor was clearly supposed to be theist the Wasp, what with being a Diabolical Mastermind who wants revenge for an offscreen prior defeat, and a blatant Sequel Hook indicating that he will return next issue, but the comic got cancelled after his debut.
The Wild CATS Wild Storm have Helspont, leader of the Cabal and one of the most powerful Daemonites in existence.