Johnny Storm isn't even the first Jonathan Storm in the Marvel Universe. That would be Professor John Storm, a scientist who first appeared in Mystic Comics #5 (1941). His sole contribution to the Marvel Universe was transforming Laslo Pevely, a man who had been injured in a car accident, into the Terror.
And of course you've got two Hanks running around (Pym of The Avengers and McCoy of the X-Men). And working together in the Secret Avengers, for more name-based confusions since they both fill the scientist role and the team is on a first name basis.
Lampshaded at one point:
Iron Man: Beast, Pym, catch the bomb! Beast: Wait, he gets to be "Pym," I'm just "Beast"? Iron Man: You're both named Hank! I have bigger problems!
In a X-Men/Star Trek: The Original Series crossover, Nurse Chapel asks for "Dr McCoy?", and both reply with "Yes?" The Beast referred to this at least once (outside the crossover), saying that whenever addressed as "Dr. McCoy, he felt the urge to say, "He's dead, Jim!"
The X-Men have two Davids. One, David Alleyne (Prodigy), is depowered and rolling with the Young Avengers, and the other is Xavier's son David Haller (Legion), who deliberately wiped himself from existence, leaving an aspect of himself in Blindfold's mind.
They also DO have 3 Steves - Steve Rogers, Stephen Strange and William Burnside who legally changed his name to Steve Rogers. Fortunately, while Captain America is occasionally called Steve, it's very rare for anyone to refer to Doctor Strange by his first name. And when they do, it's always Stephen, not Steve, most people call William Burnside by his original name rather than the name he has changed it to.
Incidentally, Marvel refuses to have two active super-heroes by the same name, in two separate collections but in the same universe. They can have, say, the Chameleon impersonating Spider-Man in his series, or a new Captain America while Steve Rogers cannot use the shield. However: When Jim Starlin wanted to resurrect Adam Warlock, the Warlock from the New Mutants had to go — and was killed in his own series. Similarly, the return of "the man called Nova" (Richard Rider) meant that the girl called Nova (Frankie Raye, herald of Galactus) was to be killed. Silly, because like many above examples, not only were the two Warlocks not related in anyway, they both had enemies called The Magus, who also were not related in anyway other than name. Although the New Mutants Warlock was named so as a homage to Adam Warlock, hence why he also had a villain named the Magus. To further the point. Adam Warlock's Magus was a possible future incarnation of himself. New Mutants' Magus is the father of their Warlock and it's their custom for the child to kill the father and then become the new Magus.
X-Man Robert "Bobby" Drake aka Iceman and New Mutant Roberto "Bobby" Da Costa aka Sunspot. There is also Barbara “Bobbi” Morse aka Mockingbird, though connected to the Avengers and not the X-Men.
Young X-Man Hope Abbott aka Trance and Hope the Mutant Messiah raised in exile by Cable.
Piotr Rasputin (who is often addressed as "Peter", "Pete" or "Petey") aka Colossus and Peter "Pete" Wisdom. This would not be particularly notable (the X-Books have lots of characters, and Wisdom never uses his full name anyway) except a) they spent a fair amount of time in the same title and b) both of them have dated Kitty Pryde. During the time when they were both on Excalibur, Colossus was generally addressed as "Piotr" or by his code-name. The two also share the name with the Marvel Universe's Peter Parker and the Trapster, formerly known as Paste-Pot Pete.
When Kitty Pryde started dating Peter Quill, aka Star-Lord, one of the character commented that she only ever dated Peters.
Magneto shares his first name, Erik, with the Black Panther villain Killmonger. Amusingly, Erik Lensherr is an alias, as Magneto's real name is Max Eisenhardt, while Killmonger's real name is N'Jadaka. There's also Erik Josten, A.K.A. Power Man, A.K.A. Goliath, A.K.A. Atlas, minor X-Men villain Erik the Red, and Canon Immigrant Erik Selvig. Going with the "Eric" spelling, Marvel also has Eric Brooks/Blade, Eric O'Grady/Ant-Man, Eric Masterson/Thunderstrike, and Eric Williams/Grim Reaper.
Early in The Amazing Spider-Man, Peter Parker dated Betty Brant while his classmate Liz Allan made a play for him. Both girls were called pet forms of the name Elizabeth. Meanwhile in The Incredible Hulk, Bruce Banner's love interest was Betty Ross; and Betty (or Betsy) Ross had also been the name of a Captain America supporting character in the Golden Age, who for a time became his sidekick, the first Golden Girl. Also from the Golden Age was Betty Dean, a love interest for Namor the Submariner. Betty Brant worked as secretary to J. Jonah Jameson, a position where after her wedding to Ned Leeds she was replaced by the rather similar sounding Gloria Grant.
There's something about "Mary" for Peter Parker: His late mother was called Mary Parker, while his Aunt May bears a name that can be a variation of "Mary". Peter went on to date and eventually marry Mary Jane Watson, the niece of Aunt May's best friend, Anna May Watson (and in the New Testament, Anna is the mother of Mary). It later was revealed that MJ's mother was called Madeline (a French variant of Mary Magdalene). And when Peter and Mary Jane had a daughter, they decided to call her May.
Penance from Generation X came back after Speedball had gone emocore and called himself Penance as well. Nowadays she's called Hollow.
In New X-Men: Academy X, there are technically two Joshes in the New Mutants squad - Joshua Guthrie (Icarus) and Josh Foley (Elixir). However, earlier in Uncanny X-Men, Josh Guthrie decided to go by "Jay" because he feels that after his girlfriend died his old name should be left in his past too.
There is a "Laurie" and a "Laura" in New X-Men: Childhood's End, but one is dead and one can't die.
X-Men used an aversion of this as part of Jubilee's backstory — her parents were murdered because her father happened to have the same name as another doctor who was involved with organised crime.
Kurt Wagner aka Nightcrawler and Juggernaut's father Kurt Marko.
Not to mention Curt Connors, aka the Lizard.
Nathan Christopher Charles Summers aka Cable, named after his grandfathers Nathaniel Essex, Christopher Summers, and Charles Xavier.
Victor Creed aka Sabretooth and Victor Borkowski aka Anole.
Brian Braddock aka Captain Britain and Charles's father Brian Xavier.
In X-Force, team director/owner Spike Freeman and team member the Spike shared a name. Lampshaded when Freeman says he really likes the Spike, and not just because of his name. This is pretty much the only time it comes up; the two share very little screen time and never even really talk to each other. Whereas the Spike was a big deal towards the end of the team's run as X-Force, Spike Freeman only became a major character after the Spike died and the book was relaunched as X-Statix.
The "no shared codenames" rule was abandoned altogether in the 2010s with the two Hawkeyes. Kate Bishop took on the "Hawkeye" identity in Young Avengers at a time when Clint Barton was believed to be dead (and very briefly actually was). However, after he made his resurrection public he gave her his blessing to continue using the identity with no "Young" or "Ms."/"Lady"/"Woman" modifier, and the two have teamed up regularly.
And this continued with Peter Parker and Miles Morales sharing the name Spider-Man, Steve Rogers and Sam Wilson sharing the name Captain America.
The Marvel Universe also has two Gladiators - Kallark, the Majestor of the Shi'ar Empire, and the Daredevil villain Melvin Potter.
Speaking of which, Sharon Ventura shares her first name with Sharon Carter, aka Agent 13.
Two people used the codename Grizzly; Theodore Winchester, an associate of Cable and Maxwell Markham, an enemy of Spider-Man. Markham himself shares first name with another Spider-Man rogue, Maxwell Dillon/Electro.
The Iron Man villains Crimson Dynamo (introduced 1963) and Whiplash (introduced 2009) are both named "Anton Vanko," but are otherwise unrelated.
Tony Stark himself shares first name with Tony Masters/Taskmaster and Anthony Ludgate/Dr. Druid.
Marvel also has Sam Wilson (The Falcon), Sam Guthrie (Cannonball), Sam Alexander (Nova) and Sam Chung (Blindspot). Lampshaded in a Nova issue where Captain America calls the Alexander household looking for Sam, and Nova assumes that he must have mistakenly called while looking for Sam Wilson.
In the series Alias (no relation to the TV series), the main character, Jessica Jones, had a run-in with another Jessica, Jessica Drew. Both Jessicas were former superheroes turned private investigators, and Brian Michael Bendis has stated that he created Jones as an Expy of Drew after he was denied permission to use the latter. This is a plot point, because another character, Mattie Franklin (former superhero turned junkie) broke into Jones' office, thinking it belonged to Drew, whom she knew and was looking for.
It also may be some Lampshade Hanging, as Brian Michael Bendis had actually wanted to write the series about Jessica Drew, but Marvel didn't want to risk her on a MAX title. So instead, the somewhat similar Jessica Jones was created and retconned into the Marvel Universe.
In Marvel Comics, Cain Marko is the Juggernaut; William Baker, alias Flint Marko, is the Sandman; Michael Marko is "Man Mountain" Marko. This wouldn't be so unusual if the last name weren't so uncommon, really.
Partially justified: Sandman changed his name to Flint Marko so no one would associate his life of crime with his mother, to protect her reputation.
One of Stan Lee's earliest creations, for Timely Comics, was the Destroyer, a superhero who operated in Nazi Germany. Later, in the early days of Marvel, he and Jack Kirby reused that name for the one-off villain in the first Human Torch solo adventure in Strange Tales. Then they reused it again for an enchanted suit of armor that Thor has to deal with. Jim Starlin muddied the waters further in the early 70s by basing the original look of Drax the Destroyer on the Timely character. And eventually, in The Invaders, the original heroic Destroyer was brought into Marvel canon as well and soon made into a Legacy Character.
Runaways has four Victors. Lampshaded when "Victor Von Doom" (Actually a Doombot, but it still counts) claims to be Victor Mancha's father, saying that "[Mancha's] mother was brave enough to anoint you with my name, but not to tell you of her dalliances as a young woman, in Latveria." The other two are evil Mad ScientistVictor Stein and his son (who goes by Chase.)
Speaking of the name Elizabeth, besides Elizabeth 'Liz' Allan, Elizabeth 'Betty' Brant, Elizabeth 'Betsy' Ross/Golden Girl and Elizabeth 'Betty' Ross, there's also Elizabeth 'Betsy' Braddock/Psylocke, Elizabeth Twoyoungmen from Alpha Flight and Elizabeth Guthrie.
Jennifer Walters/She-Hulk and Jennifer Takeda/Hazmat, as well as Jennifer Kale and Jennifer Stavros/Roulette.
The Ultimates: Not Thor himself, but Mjolnir. The Ultimates 3 has him suddenly go from using the axe-hammer version to one more like regular Thor's Mjolnir. Ultimate Comics Thor covered it by revealing they're separate hammers, which just have the same name.
