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.
Speaking of which, Albert Wesker wants to use the Uroboros virus to rule the world. Strangely enough, Master Albert wants to use the Ouroboros Biometal to do the same thing.
Here are 2 more Alberts. First, there's a certain mad scientist bent on (you guessed it) ruling the world. And then, let's not forget the Axe Man from Resident Evil Outbreak: File #2. For all future references, if a character is named "Albert" and he's a Capcom character, chances are that he'll definitely be a villain.
The trend continues with yet another Albert, this one a homicidal scientist representing the sin of greed.
Balrog: The American Boxer in the U.S. or the Spanish Ninja in Japan. Neither has anything to do with a certain anthropomorphic bar of soap from Cave Story.
Vega: The Spanish Ninja in the U.S. or the Man in Red in Japan.
M. Bison: The Man in Red in the U.S. or the American Boxer in Japan.
The reason the names were switched around is because Capcom was afraid Mike Tyson would sue them if a black boxer named "M. Bison" appeared in an American video game. Additionally, when the designers presented the game to Capcom USA's marketing department, they believed that the name Vega was a weakling's name and didn't fit the Dictator's character.
To prevent this confusion, they are internationally called "Dictator", "Claw", and "Boxer", respectively.
A much more obscure fact is that Capcom has two other protagonists named "Ryu", upping the total to eight: Other than the six mentioned above, there's also Ryu from Avengers (aka Hissatsu Buraiken) and Ryu from Trojan (Tatakai no Banka). Incidentally both games were designed by Takashi Nishiyama, who took the name "Ryu" from the kanji in his given name.
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.
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.
Played with in Shin Megami Tensei IV: the Player Character and his best friend Issachar hail from the village of Kiccigiorgi, which, when spelled in Japanese, reads "Kichijouji", the same name as the neighborhood where the protagonist of the original Shin Megami Tensei came from.
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. Also, they both want to murder their family members. (Kazama kills out of revenge, Kisaragi however kills out of a Yandere psychotic obsession.) Now you'll need to be careful if you ever named game character "Jin K."
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.
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 interesting 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!
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 the Final Fantasy series. 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; his voice actor, Tomokazu Seki, also did the voice of Gilgamesh in the The Tower of Druaga anime.
This is the entire reason why the latter two met in a room
Bahamut: Extra-powerful dragon throughout the Final Fantasy franchise? Gigantic tank from Battle Bakraid? Or massive hippopotamus-headed dragon-fish from La-Mulana? (Note: The last Bahamut is much more faithful to the original concept from Arabian folklore.)
Kaboom: Atari2600 bomb-catching game, or Adobe Flash suicide bombing game?
Moresby is the city setting of Dead Island and portrayed as similar to run down Los Angeles or projects some cities have. Morseby is also a real village in Papua New Guinea (the game uses the fictional Banoi as an Expy and so run down it doesn't even have running water.
Marvel vs. Capcom 3: In Ryu's ending, the screen says the next match is between Ken and Mr. X. Mr. X is the name of Tyrant in Resident Evil 2, an alias of Dr. Wily, and the name of a character from the Marvel comic Thunderbolts, who is also a Wolverine villain. Given that the ending is set in the Bloodsport tournament in Madripoor, it's safe to say it's the latter they're talking about (who has faced Wolverine in Bloodsport before).
Marvel also have their own character named Firebrand.
With Ultimate's new characters announced, we also have Phoenix, a.k.a. Jean Grey, and Phoenix Wright. The game solves this problem by having most of the characters call him "Mr. Wright."
The above is Lampshaded by The Hulk of all people.
Hulk: Puny man not Phoenix! Phoenix a bird lady. Hulk confused.
Also, Maya is the name of Phoenix Wright's assistant and C Viper's real name.
Here is a quote by Spider-Man, referring to Felicia Hardy (Black Cat) after he defeats Felicia from Darkstalkers:
Spider-Man: "What is it with me and cat women named Felicia? Jeez."
Supplementary material included with TIE Fighter mentions that the player character of that game was given a code phrase to use whenever he wanted to speak in private with a specific superior officer. That phrase was "There's a fog over Celadon City".
Brutal: Paws of Fury features The Dali Llama, of no relation to the real world's Dalai Lama. For one, the video game's version is an actual llama. Second, he's a martial artist founding a tournament based around fighting.
Jay's Bar is a bar in which Ryu Hayabusa fights the Barbarian in the Original Trilogy. And there's J's Bar, a bar in Raccoon City in which eight unfortunate souls find themselves caught in a zombie outbreak. Interesting enough, the former is designated J's Bar in the Original Trilogy.
It is also the name of an Early AI software which attempts to emulate a psychiatrist, which some people considers a game.
HiramBurrows staged a coup d'etat, organising the assassination of a benevolent queen. Hiram Barows, on the other hand, died fighting in a civil war resulting from a succession crisis between two selfish would-be queens.
Strife can be: a 1996 action-RPG remastered and rereleased in 2014, or an unrelated upcoming (as of February 2015) game. To make the confusion worse the "Encyclopedia Gamia" wiki gives the name without disambiguation to the latter game, although since the former is older and still available, it should be the one which isn't disambiguated.