The Arrow is a Centuar comics character revived in Project Superpowers, a member of the Protectors in Malibu Comics, a hero in Legion Unleashed by Raven Entertainment, and the Arrowverse alias of Oliver Queen. Arrow is a Green Arrow inspired foe in The Legion.
Backlash is a former member of Team 7 and Stormwatch, a foe of The Ultraverse character Warstrike, and a foe of the Justice League Task Force and Freedom Fighters.
Blue Marvel is the alias of Adam Brashear. In Quasar, the 1950's Marvel Boy and an impostor of Marvel Boy both appeared as Blue Marvel.
There are two popular comic strip characters known as Dennis the Menace: the American one created by Hank Ketcham, and the UK one featured in the anthology comic The Beano. Both are young grade-school boys who own dogs and get into mischief, but they're otherwise quite different. To make the coincidence even more astounding, the characters first appeared (in different publications, on opposite sides of the Atlantic) within three days of each other in March 1951.
To avoid confusion the American verison is "Dennis" in the UK and the British comic is called "Dennis and Gnasher" outside the UK.
DC and Marvel each have a character named Atom Smasher (typically differentiated by the Marvel one being Atom-Smasher). In DC, he's the size-changing grandson of the energy-projecting villain Cyclotron. In Marvel, he's the energy-projecting enemy of the size-changing hero Black Goliath.
There's The Sentry, a superhero and former Avenger, and the Sentries, a group of giant robots who serve the Kree.
The two Captain Marvel's.
Only two? Billy Batson, the Lieutenant Marvels (all three of whom happened to share the name "Billy Batson" with the original) Mary Batson, Freddy Freeman on one side, and Mar-Vell, Genis-Vell, Phyla-Vell, Monica Rambeau, Khn'nr and more on the other... Granted, most of them have alternate names.
To add to the confusion, Monica Rambeau and Genis-Vell have both used the name Captain Marvel and Photon. They at least consciously made the swaps together so you didn't have both using the name at the same time.
There's the alien android who said SPLIT! Who, in what is surely a complete coincidence, had a young friend named Billy Baxton.
Aaannd we have the name Marvel Boy which has been used by a member of the New Warriors (who had an Alternate Timeline double to make things weirder), a teen Marvel superhero from the 50's, and a current Kree hero who is part of the Young Avengers. Marvel Boys have nothing to do with Captain Marvels, though. Neither does Jean Grey who once went by the name Marvel Girl.
That said, the 1950's Marvel Boy had powerful Quantum Bands which eventually went to the hero Quasar who also very briefly took the name Marvel Boy before settling on Quasar. The Phyla-Vell Captain Marvel adopted the name Quasar for a while.
Now that we have the whole Captain Marvel/Photon/Marvel Boy/Quasar thing sorted out, let's turn to Ms. Marvel. Ms. Marvel, Carol Danvers, was the Distaff Counterpart to Captain Mar-Vell. The name was also taken up by another woman, Sharon Ventura, who briefly joined the Fantastic Four during the period where the original Ms. Marvel was operating with the Starjammers under the name Binary. Ventura would later abandon her claim to the name and fully adopt the moniker She-Thing, while after returning to Earth and rejoining the Avengers, Danvers operated for a time under the name Warbird before returning to Ms. Marvel. During Dark Reign, Moonstone (Karla Sofen), a member of the Thunderbolts and herself a Distaff CounterpartLegacy Character (Karla stole the identity from the original Moonstone, Lloyd Bloch), took the name Ms. Marvel as her identity in the Dark Avengers.
And more recently, the former Ms. Marvel has taken up the Captain Marvel mantle herself. Which has in turn caused Marvel to recycle the Ms. Marvel identity for a new character named Kamala Khan. She was inspired to be a hero by the original, but other than that there's absolutely no connection between the two.
Also worth noting that one should not confuse Carol Danvers with Linda Danvers.
Gladiator is a Daredevil villain, and a member of the Shi'ar Imperial Guard.
Glory is an Amazonian, a waitress, or an alien in Image Comics, and a member of the Warriors of Plasm in Defiant Comics.
Miss America is the Golden Age alias of Madeline Joyce, and the modern day alias of America Chavez.
Multi-Man of DC Comics (debuted 1960) and Multi Man of the Impossibles cartoon (debuted 1966) have surprisingly different powers.
John Dee is a villain in Night Raven, a mutant in the Stridex X-Men Marvel Collector's Edition comic, and an unrelated mutant first appearing in Son of M. John Dee is the alter ego of DC Comics villain Doctor Destiny.
There have been multiple identities of Spider-Man's somewhat "Distaff Counterpart" Spider-Woman: Jessica Drew (black haired, wears red, can float, super power reels more about spider venom), Julia Carpenter (blonde, wears black, can float, her super power is more similar with Spidey although she shoots psionic energy webs), Mattie Franklin (seems to be very-directly inspired on Spidey himself, uses spider-legs), and Charlotte Witter (Villainess, white haired, wears green-yellow (a bit like Rogue)). And the Marvel Mangaverse turns Mary Jane into this. There was a Golden Age Spider-Woman in Major Victory #1 by Dynamic Comics.
DC Comics has a Batman villain named Scarecrow and Marvel Comics has a villain named Scarecrow (who bounces around Iron Man, Spider-Man, and Ghost Rider's rogues galleries). They even teamed up in Marvel Vs. DC. There is in fact another Marvel villain known as Scarecrow, but now referred to as Straw Man.
For whatever reason, Green Lantern Hal Jordan happens to share a name with his own cousin, Harold "Hal" Jordan, alias Airwave. Yeah, what?
There's also a Hal Jordan who appeared in a Golden Age Timely's Submariner Comics issue, ten years before his more famous namesake's debut. Curiously enough, he's also an aircraft pilot and looks similar to Green Lantern.
Changeling is either: a minor X-Men adversary from the 1960's who underwent an off-panel Heel–Face Turn and died while covering for Professor X; or another name for Teen Titans member Gar Logan. Both have shapeshifting abilities, but they function differently from each other (the former can change into other people, while the latter can transform into animals).
Morph from the 90's X-Men animated series was supposed to be a modernized version of Changeling, since he technically was an X-Men member in the comics, even if it was only established through a retcon. He even had the same civilian identity of "Kevin Sidney", but the codename "Changeling" couldn't be used at the time since it now belonged to the DC Comics character. Ironically, when the Teen Titans got their own animated series, Gar Logan went back to using his old Beast Boy handle. By that time, the Morph name had pretty much stuck for the Marvel character, with his Alternate Reality versions from Age of Apocalypse and Exiles using that name.
Magneto is both an incredibly popular villain/Anti-Hero from Marvel and an extremely obscure Aquaman villain from DC.
In the 1976, Teen Titans introduced a black female member named Bumblebee who could turn herself small, fly and sting bad guys. Years later in 1984, Marvel began publishing Transformers comics, and had been instrumental in developing the characters, hence why I can put them under comic books, and as we all know, there was an Autobot named Bumblebee who would turn into a Volkswagen.
Nightwing used to be known as Robin, but Nite-wing is a mentally ill man who got his name from a sign advertizing chicken wings all "nite". The latter was a supporting character in the former's series. Nightwing is also the alias of Van-Zee the Kandorian.
Dr. Hugo Strange is both a Golden Age hero and a Batman villain, but neither is to be confused with Marvel's Doctor Strange, who himself should not be confused with one-off Silver AgeIron Man villain Dr Strange. When the GA hero Strange was used in Tom Strong, his name was changed to Tom Strange, probably in part to avoid confusion and otherwise because he was in that story the alternate universe counterpart to Tom Strong.
For whatever reason, Malice is very popular villain name. We have:
In the Avengers annual where future X-Men mainstay Rogue first appeared, a little girl, apropos of nothing, introduces herself as "Maddy Pryor," adding "I been sick, but I'm better now." A little while later, X-Men leader Cyclops begins dating - and soon marries - a woman named Madelyne Pryor. Readers assumed there had to be a connection between the two. Actually there wasn't. In real life, Madelyne Prior is the name of a singer with the British folk rock group Steeleye Span. Chris Claremont - the writer of the stories in question - liked the band and used the name as an homage twice, for two otherwise unrelated characters.
Similarly, before the Jubilee we know debuted, there was an unrelated one-shot character with the same name and power (and introduced herself with a similar line.) Evidently, it was a "wanted to reuse that character, but it wouldn't work with the way the older story ended" case.
Fleetway Comics published stories about a kid who played practical jokes on people called...wait for it...The Joker. No comment...
Speaking of Golden Girl, the original's civilian identity is Elizabeth Ross, who went by "Betty" for some time, no relation to Bruce Banner's frequent love interest.
Same goes for the Angel. The first is a Badass Normal costumed detective during the Golden Age, while the much more popular one is Warren Worthington, the Winged Humanoid member of the the X-Men.
An early Incredible Hulk one-time villain, Mongu, was a hulking "space barbarian" who turned out to be a Russian agent operating a Mini-Mecha designed to look like a space barbarian. Hulk trashed the armor and sent the agent, Boris Monguski, packing. Years later, Man-Thing encountered an actual barbarian named Mongu in a gladiatorial contest in Mongu's home dimension. The Maha Yogi would later bring Mongu to Earth to fight the Hulk and Doctor Druid.
In the Knightfall series of Batman there is a Dr. Simpson Flanders. (No word on whether he greets himself every morning and then tells himself to shut up.)
Though Word of God is that the robot Vision was created as an Expy when Roy Thomas was denied permission to use the original. The name and costume are meant to be a Shout-Out to the Golden Age version.
There seems to be no relation between Cain Marko (aka The Juggernaut) and Flint Marko (aka The Sandman), apart from the fact that both have fought Spider-Man and were co-created by Stan Lee. Flint Marko's name has since been retconned to be an alias.
Speaking of which, Marvel's Sandman has nothing to do with the several DC characters who go by that name (such as Wesley Dodds or Morpheus).
The 1940s Timely Comics heroine Black Widow is definitely not the same character as the more familiar Marvel Comics Russian spy hero of the same name.
And neither of them have any connection with the Battletech character, the Black Widow who leads the eponymous mercenary sub-unit in Wolf's Dragoons. Although both Natasha Romanoff (Marvel) and Natasha Kerensky (FASA) are both extremely attractive Russian redheads who are dangerous to those who cross them...
We have Daredevil, a Marvel superhero from the sixties who is blind, but has supersenses, wears a red devil-like costume, and fights with a billy club . We also have Daredevil, a Lev Gleason Badass Normal superhero from the forties who wears a red-and-blue costume (split down the middle) and is very good with a boomerang.
In Marvel Comics, Hamilton Slade is the real identity of the third Phantom Rider, a modern day descendant of Carter Slade. Hamilton Slade is also an 18th century vampire in the Marvel miniseries Apocalypse vs Dracula.
There is a G.I. Joe character named Ghost Rider. When Marvel was publishing G.I. Joe comics, they didn't want the trademark getting confused, so his name was never use (there was a running gag that nobody could ever remember his name). Now that IDW is publishing it...the running gag is maintained, because Marvel still owns the trademark in comics.
This is going to be a plot point for the Sonic the Hedgehog/Mega Man crossover Worlds Collide when Shadow Man meets the Roboticized Master Shadow Man, who resembles Shadow the Hedgehog.
Victor Zsasz is the name of a serial killer that Batman deals with occasionally. Charles Victor Szazs is the real name of Vic Sage, The Question. Not quite the same thing, but very close. (Both were named after the psychologist Thomas S. Szasz.)
Years before Jean Grey began calling herself "The Phoenix", Phoenix was actually the short-lived identity used by Helmut Zemo before he settled on becoming the new Baron Zemo.
In a bizarre coincidence, Luke Cage and Captain America both have two separate villains named Diamondback and Cottonmouth. Luke's Diamondback and Cottonmouth are street level villains (and both male), while Cap's Diamondback and Cottonmouth are superpowered members of the Serpent Society (and Diamondback is a woman).
This is the reason why Spider-Gwen is titled the way it is. While canonically her hero name is "Spider-Woman", we already have a Spider-Woman - Jessica Drew. It's also a Fan Nickname that went canon.
An aquatic superhero debuted in World War II. He was the last survivor of an underwater civilization (and royalty to boot), had superior strength, and fought the Axis. If you're thinking it's Namor, you're wrong. It's Iron Man.
Supervillain Thanos shares his name with a villain in french comicbook Lanfeust and they're both ruthless conquerors.
The second Robin's full name is Jason Peter Todd. The Golden Age Flash, whose identity was public and who lived as a hero long before Jason was born, is named Jason "Jay" Peter Garrick.
In a 1966 story by Jack Kirby and Stan Lee, a hallucinating Captain America sees several old enemies of his and identifies one of them as Agent Axis. Kirby had indeed created a Nazi villain with that name back in the 40s, but it was during his time at DC. Roy Thomas later addressed this apparent mistake by creating a distinct Agent Axis for Marvel, using him in The Invaders. And shortly afterwards, DC reused the name for another apparently unrelated Nazi.