The Nobodies from Devil May Cry should not be, under any but the most heavily drugged-and-drunk situations, mistaken for the Nobodies from Kingdom Hearts. Though a properly done DMC/KH crossover would be totally sweet.
Both Paper Mario and Wario Land The Shake Dimension have near identically named volcano levels with a general Lethal Lava Land theme. One's... Mt. Lavalava, and the other is Mt. Lava Lava.
A much more obscure fact is that Capcom has 2 more main characters named "Ryu", upping the total to 8: Outside of the 6 mentioned above, there's also the protagonist for both old arcade games Avengers (known in Japanese as Hissatsu Buraiken) and Trojan.
The Big Bad of Data East's Karnov is a hydra-type dragon named Ryu.
Tsukihime and Tales Of Hearts both have a pair of siblings named Kohaku and Hisui. In the former, they are (female) identical twins and Kohaku is the older one, whereas in the latter they are not twins and Hisui is Kohaku's older brother. Like the above Ryu example, only one of these pairs (Tsukihime's) is No Last Name Given, though.
While we are on the subject, has Kohaku and Kohaku met the young lad Kohaku yet?
Moo Moo Farm is also the infamous secret cow level in Diablo II.
Rainbow Road in Mario Kart and Rainbow Road in F-Zero X (The 64DD Expansion Pack even has a remix of MK64's Rainbow Road music). Super Mario 64 also has a secret stage called Rainbow Ride.
Another same company example: an F-Zero racer and Fox McCloud's father both share the same name: James McCloud (It should be noted that the former is technically a Shout Out to the latter).
Dr. Carroll appears as name of a computer in Perfect Dark and as name of a scientist in the prequel. The former is implied to be a Virtual Ghost of the latter.
Both of these are references to an obscure Greek God (really obvious in the God Of War case), a god of strength, who just became an aspect of Zeus later on.
Kratos Aurion even has a title in his game named "War God".
In the Japanese version of the first Mega Man game, the Robot Master known as "Bomb Man" elsewhere was originally known as "Bomber Man". This was changed in the overseas version to avoid confusion with the much better known Bomberman.
World of Warcraft has Xavius, first of the satyrs and X'avius, a Scourge necromancer. While the satyrs are very found of naming places or themselves after their master, there is no connection between him and X'avius.
Kid Icarus has the "Kometo" (sometimes transliterated as "Komayto") enemy type; Iji has the "Komato" aliens.
Do not confuse the Nineball and the AC Nineball. The first is an idiotice fairy who somehow became an Ensemble Darkhorse (and Nineball is her nickname, anyways), and the second is a RecurringBonus Boss whose mere appearance on the battlefield is considered by many players to be a Oh Crap moment and reason enough to consider the Godzilla Threshold crossed (and as a result, time to do anything you can to kill that AC, regardless of normal play style).
Beat happens to be a speedy guy who lives in a trendy alternate Tokyo. Am I talking about the protagonist of Jet Set Radio, or his partner in The World Ends With You?
And then there's Beat, the avian robot from the Mega Man series, and a young wielder of firearms in Eternal Sonata.
Iris is the ex-girlfriend of a Capcom character, whose relationship with said character ended with a tragedy. Is she a robotgirl, or a shrinemaiden?
Unless, of course, she's actually [[Erim, the Sinistral of Death in Lufia II.
Speaking of Gradius: is Cruiser Tetron a boss in Life Force, or the Big Bad of Hero Core? However, this one is intentional, since Daniel Remar came up with the story of the latter game as a child and named the villain after said boss.
The Boss, either the way too patriotic Badass lady from Metal Gear Solid 3, or the way too violent Badass player character from Saints Row 2 (who can also be a lady if the player wants). In La-Mulana, it's the name of the blue enemy unique to Hell Temple (and the avatar of one of the game's creators). It's also the name of the Big Bad from Jumper Two.
There's a character in BlazBlue who plays with this trope with her first AND last name. Her name? MakotoNanaya.
In BlazBlue, there's also Jin Kisaragi, a cold-hearted asshole... and in another game, there's Jin Kazama, a cold-hearted Tragic Hero. Both like keeping people away from them. Now you'd need to be careful if you ever named a game character "Jin K."
Gene from God Hand is the male Player Character, who specializes in Good Old Fisticuffs, reversing enemy wrestling movies and dodging enemy attacks instead of blocking them. Jeane from No More Heroes is the female Final Boss, who specializes in Good Old Fisticuffs, reversing your wrestling moves, and dodging your attacks instead of blocking them.
Jeane is also the Ms. Fanservice magician from the Suikoden series.
That one's more down to odd romanization (wouldn't be the first time - Hello Seifer). FFX's Rikku is spelled Ryukku in kana.
This trope is at its most egregious in Final Fantasy IV, which boasts two Prince Edwards (who have absolutely nothing to do with each other) as major playable characters in the exact same game. One is Prince Edward Chris von Muir of Damcyan (who, to be fair, was called "Gilbert" in the original Japanese version), and the other is Prince Edward Geraldine of Eblan (who goes by "Edge" anyway).
Mercer as a villain in science? Do you mean Dr Mercer from Dead Space or the real Alex Mercer of Prototype?
A character named Sora who eventually gets an alternate self: Sora! Roxas!Haseo! Wait...
An immense space station with picturesque plant-heavy corridors, cityscape-like views out of the windows, lots of residential modules and offices connected together, and the second location the player visits in the game, before Opening the Sandbox. You're thinking of Citadel Station from Knights of the Old Republic II... or perhaps Mass Effect. There's also a Citadel Station in the first System Shock.
But not the Citadel from Half-Life 2, which is a massive Combine facility. That thing is downright scary inside.
Maki had her name changed to Mary in both Revelations Persona and Kira Kira Pop Princess. There is also a Tammy in both, but the former's Japanese name is Tamaki while the latter's is Tamae.
The Disgaea series has two angels named Vulcanus: The main antagonist of the first game and the female lead of the fourth game.
Scorpion from Mortal Kombat is not to be confused with The Scorpion, a masked wrestler from Capcom's short-lived Saturday Night Slam Masters series (although his Japanese name is Astro).
Or the fact that it was Lance Bean's nickname in the American versions, up until Contra 4, where a new character was given the nickname.
The Mother antagonists from Wild ARMS and from Rogue Galaxy are both major villains, with world eater tendencies, and both have insect-like characteristics (Mother from Wild ARMS was trapped in a cocoon; Mother from Rogue Galaxy looks like a praying mantis in her first form, before her shell cracked and then turned into a moth-like creature).
Fennel is a glasses-wearing side-character researcher, that much is certain. Question is, is she amiable and generous in generally peaceful Unova, studying the dreams of Pokémon, or is he a misanthropic Mad Scientist who Looks Like Orlok while studying Thaumatech in the warring state of Alistel? Both games were released at about the same time, too, making the parallel even more amusing.
Games of American McGee's Alice seem to use the name The Red Queen to refer to the Queen Of Hearts and the red queen chess piece interchangeably.
A rather insteresting example with Sheena: both a minor character from the NES Strider and the female playable character from Run Saber, which is itself an Expy of the original arcade/Mega Drive Strider!
Don't confuse Beatrice and Beatrice. Even though they are both mental entities, of a sort.
Shadow's a generic name, but ironically only two may come to mind: One's a hedgehog, the other's a ninja.
More a What Could Have Been example, but in Pokémon Gold and Silver , the protagonist's home of New Bark Town was originally going to be named "Silent Hills". Nearly a year before their release, the game Silent Hill came out, which may have lead to the rename.
This Starman makes you invincible for a few seconds. That Starman is a servant of Giygas. Star Man might also be the Robot Master from Mega Man 5, or the Masked Luchador from Pro Wrestling.
Destruction Derby is both the name of an early arcade game by Exidy (also known as Demolition Derby) and a PlayStation racing game series.
Jean and Paul. Both are antagonists there to distract the player from what's really going on. Jean is a smug and fairly flamboyant man just taller than the main character with a hat that rival's only the protagonist's in pimp-level per cubic centimeter, and his eyes are covered atall times. Paul, meanwhile, is a much less attractive man with an amazing gift for inventing fantastic machines. They're both trying to get in the way of an amazing archaeologist with a costume that's entirely unmistakable as a dark coat and top hat... the question is, is that man Doctor Lautrec or... (sigh) Professor Layton? Come on, Konami.
Gilgamesh is either the prince who wore golden armor and attacked monsters to save Ki in The Tower of Druaga or the weapon-collecting Recurring Boss from Final Fantasy V. Both Gilgameshes are interested in a sword called Excalibur, though they might get the bad version instead. There's also the Nasuverse Gilgamesh who also wears golden armor and would like to wield Excalibur, though it's usually wielded against him.
This is the entire reason why the latter two met in a room
