Hotel Dusk: Room 215 has Mila, who is the name of a girl staying at the hotel who shares her name with Bradley's dead little sister.
Secret of Mana has a character named Phanna, and a separate character named Fanha. This is entirely coincidence, and no attention is brought to it.
Given the 500ish characters that have appeared in the Suikoden series so far, it's something of a miracle that there were only a handful of names (Hugo, for one) ever shared by multiple characters (time-traveling teleportresses in Suikoden III aside). Then there's Sarah the evil blond sorceress and Sarah the level 50 cleaning lady.
In Tactics Ogre, there are two Lans (Lanselot), one on the protagonist's side, and one on the antagonist's. Both are Knights, and the first stage in the game involves confusing one for the other. The prequel reveals that this is a title.
There are two robot masters named Oil Man, Wave Man and Blade Man in the Mega Man series. All three of the originals are from the fairly obscure PC games not made by Capcom.
The series has six characters whose names are variants of John - Naked Snake (real name John/Jack), Raiden (aka Jack the Ripper), Little John (Raiden's son), Johnny "Akiba" Sasaki, Akiba's grandfather (also named Johnny) and Ivan Raidenovitch Raikov, plus two more of the similarly-sounding Jonathan (a Soviet soldier in MPO and a member of Rat Patrol 01 in MGS4).
The same series also includes two Davids (Solid Snake and Zero), Jim (Houseman) and James (Johnson), Natasha (Marcova) and Nastasha (Romanenko), two President Johnsons (the real-life Lyndon Johnson and the fictional James Johnson), four Georges (Kasler, Sears, the orphan in MGR, and Code Talker), two Boris (Volgin and Popov) and no less than five characters who have at some point gone by the codename Snake (Naked Snake; his clones Solid, Liquid and Solidus; and his body double Venom).
In the later versions of Metal Gear 2, Natasha Marcova was renamed Gustava Heffner, long after said character was already referred by her original name in the plot summaries included in the first Metal Gear Solid.
Les Enfants Terribles, the name of the government project that led to the creation of Big Boss' sons, was also the name of Running Man's former terrorist outfit in Metal Gear 2
Then there's the members of the B.B. Corps in MGS4, who were deliberately named after the deceased members of FOXHOUND from MGS1 (Octopus, Raven, Wolf and Mantis).
Bombastically averted in Dynasty Warriors, at least for the English editions. Chinese naming system back in the day was very simple, consisting of only one, or very rarely, two hanzi as surnames, and exactly one hanzi as a given name. The given names are mostly two in the modern day, but the series is an adaptation of Romance of the Three Kingdoms, which is set in an era where it's practically forbidden for you to take more than one hanzi as given name (seriously). The Japanese version actually averts this since the hanzi of the characters are mostly different, despite the fact that their pronunciation of the hanzi is actually much more homophonous than any other languages can hope for, and the English version would too, if it weren't for the fact that it uses the Hanyu Pinyin diacritical transliteration (which transcripts a lot of hanzi using the same letters) without using the diacritics themselves. Many of the newly-initiated, before they even play the games themselves, are probably already stumped in how to memorize which character is which.
There are 6 characters with the surname "Zhang" alone: He, Liao, Chunhua, Jiao, Bao, and Fei, of whom only the latter two are related to each other. That's because it's one of the most common Chinese and world surnames ever, so it's understandable that there are many people who have it without being related.
There's three characters in Wu with the surname "Lu" (Xun, Meng, and Su). None of them are related to each other. And no, they aren't related to Lu Bu, either.
Xu Zhu and Xu Shu. Thank God they're from different factions.
How about Yu Jin and Yue Jin? Miss one letter and you now refer to an entirely different character. Oh, and this time, both came from the same faction.
Xingcai has an older sister who has the same name as her (actually, in the novel, both of them are referred as just "Empress Zhang (older)" and "Empress Zhang (younger)"). This actually becomes a pop quiz in Dynasty Warriors 7.
Kingdom Hearts faced this problem when they added Pirates of the Caribbean to their cast of Disney Worlds, now having TWO playable characters named Jack. (Jack Sparrow, from the aforementioned movie and Jack Skellington from The Nightmare Before Christmas). Since this would have interfered with the games level-up system for additional party-members, the pirate-Jack is referred to as "Sparrow" in the game's pause-menu and level-up boxes; interestingly, Sora, Donald, and Goofy also call him "Captain".
And when a version of Rikku from Final Fantasy X turns up, they simply don't call her anything, to avoid confusion with the original character Riku. This is actually why Yuffie is with Leon in the first game: the original plan was to have Rikku accompany him, but the powers that be decided it'd be too confusing with two Rik(k)us.
Not to mention where this is done in the plot. Mickey spends much of Kingdom Hearts II searching for Ansem to request his help. No, not "Ansem: Seeker of Darkness", the villain from the first game, but "Ansem the Wise" (AKA: DiZ), who the villain of the first game actually stole the name from after deposing him. The villain's real name is Xehanort, which soon leads to....
And then, of course, there's MASTER Xehanort- who's actually the same person as the Xehanort calling himself Ansem: Seeker of Darkness, before he played Body Snatcher with Terra. Basically, most instances of this trope in the Kingdom Hearts series are really just Master Xehanort messing with our heads.
The Kingdom Hearts wiki refers to Ansem (the evil one) as "Xehanort's heartless".
In the Might and Magic series, there are multiple characters called Crag Hack, Sandro, Corak and so on. Lampshaded during the good ending of Might and Magic VII. Subverted in Might and Magic I and Might and Magic V, both have a character called Alamar. The subversion is that in the first game Alamar is imprisoned by Sheltem who then impersonates him, while in the fifth game Sheltem appears on another world and just calls himself Alamar to hide his true identity.
Usually played straight by necessity, though, as few characters have a (known) last name.
Corak twists it around further: where the others (including Alamar — another shows up in the Heroes series) are different characters that happen to share a name, the Coraks are robots, with Corak being the name for the model.
A rather confusing example turns up in Heroes of Might and Magic V. Despite being a new setting, the game refers to a Sandro several times. From what little is known, he seems to have a lot in common with the previous characters named Sandro.
Might and Magic VIII features a minor character named Archibald, just as the Big Bad of Heroes II and otherwise recurring character Archibald Ironfist. Apparently Archibald Ironfist has made the name 'Archibald' impopular in certain quarters, so the VIII-Archibald (named Archibald Dawnglow) is doing his utmost to be a Good Guy to show that he's nothing like that other Archibald.
Enroth (the setting of Heroes I to III and Might and Magic VI to VIII) had two relatively important mainly backstory characters named Ethric: Ethric the Mad, a mage who invented the lich process and became the first lich on Enroth, and Ethric, a warlock who once was Sandro's mentor and later became a lich. It is likely that they were originally intended to be the same character, but for continuity reasons this was made impossible by Shadow of Death (Sandro's mentor shows up perfectly alive at a point when liches have been around for at least a decade).
Averted in JoJo's Bizarre Adventure: All Star Battle: the protagonists of Parts 4 and 8, both named Josuke Higashikata, are playable characters. The Japanese version of the game spells their names with different kanji, while the western version places a "4" and "8" at the end of their names to differentiate them by the Part they appear in.
In the games since Pokémon Gold and Silver, the individual, nondescript Trainers you fight all have unique names. While few of them share names exactly, you'll often run into two totally different Trainers with slight spelling variations in their names, such as an Allie and an Alli, or a Sean and a Shawn. This is at its most amusing in Platinum, where there's a Zackary (a Camper) and a Zachary (a Fisherman) on the same route.
Of course, somewhat realistically given the completely different settings, this happens quite frequently across different games. For example, in FireRed and LeafGreen there's a Bug Catcher Colton, and in Pokémon Diamond and Pearl there's a Swimmer Colton.
The Spanish translations of the game averted this twice: First in Pokémon Gold and Silver, where two of the trainers who gave you their phone were called Ángel (The game called them "Ángel1" and "Ángel2".), and in Pokémon Ruby and SapphireBrendan was renamed "Bruno", just like the Elite Four Trainer, who kept his name in the Spanish version as in English and is even referenced in-game. At least the former was fixed on the Updated Re-release, where the second guy was simply renamed Ángelo, making one wonder why they didn't come with that the first time around.
It was also rather close to being averted with a major character in the English version of Platinum - the Frontier Brain Caitlin differs by just one letter from a generic trainer on Route 203, Kaitlin. Their Japanese names (Cattleya and Sayuri respectively) aren't similar.
Typically a name used by a major character never gets reused in subsequent titles (to the point that Ace Trainer Ariana in Pokémon Diamond and Pearl was already changed to Moira in Pokémon Platinum due to the name being saved for a Rocket admin in Pokemon Heart Gold And Soul Silver), but names have slipped through; Pokémon Gold and Silver has a Firebreather Bill (named after the original Pokemon Storage creator), and the Gen IV games have a Parasol Lady Sabrina (named after a Gen I Gym Leader.)
This was also the reason why the 3rd Generation-introduced move called Comet Punch in Japanese had to be localized as 'Meteor Mash', because the English localizers had already used the name 'Comet Punch' for a 1st gen move. (Which was 'Consecutive Punch' in Japanese, but that would have broke the character limit) Unfortunately, this lost the implication that it was a punching move and thus boosted by Iron Fist. (Nothing with Iron Fist actually learns Meteor Mash, but that's beside the point.)
The same thing happened again in Gen 5 with Low Kick ("Kick Down" in Japanese) and Low Sweep ("Low Kick" in Japanese).
In an example that reaches across the entire series, in Generation II, the seventh Gym Badge, called the Ice Badge in Japanese, was renamed Glacier Badge. But then the seventh badge in Generation IV was named Glacier Badge in Japanese, so it was changed to Icicle Badge. But then after that, the seventh Badge (seeing a pattern yet?) in Generation V was named Icicle Badge in Japanese, so it had to be changed to Freeze Badge! Whew...
Averted in the French translations, where Brock and Steven Stone are both called Pierre (the latter being known as Pierre Rochard in later games).
Pokémon FireRed and LeafGreen have a minor trainer named "Dawn", which is also the name of the female protagonist of the Sinnoh games.
Aeon the time traveler (Castlevania: Judgment) and Aeon the fat chef (Castlevania: Order of Ecclesia). Because both games released at the same time (and even had DS-Wii connectivity), some people were led to believe that Aeon in Ecclesia would be the time guardian from Judgment.
And Elisabetha (Dracula's first love), Lisa (Dracula's second love and Alucard's mother), and Elizabeth (Dracula's niece and servant in Bloodlines).
In Runescape, there are several Alis, several Petes, several Jacks and also few Bobs, Sarahs, Brians and Charlies. There are few other repeating names too.
Parodied with Alis and Petes. All Alis, for an example, come from Pollivneach and some don't like to be called Ali. For other names, the similarity is just a coincidence.
And, while not exactly names but instead titles, the Mysterious Old Man, the Strange Old Man, the Weird Old Man, and the Odd Old Man. The Wise Old Man is a borderline, since his title isn't a synonym for "strange" and he does have a real name.
Elite Beat Agents has Sofie Hudson the weather reporter and Sophie Keen the supermodel.
In Shin Megami Tensei, the law hero's girlfriend is arrested when the government rounds up everyone with the same name as the heroine. One character wonders how many people with that name there can be.
In Persona 4, playable character Kanji Tatsumi shares a name with Tatsumi Port Island (the location of Persona 3), which the characters visit at one point. In Japanese they're written with completely different characters that just happen to be pronounced the same way, but there's no distinction between them in the English version.
Probably a whole load of other name-alikes that we have missed in this list.
In Ever17: no two characters actually share the same name, but the names that the player initially knows them as can sometimes be one of several characters. "You" could be either Youbiseiharukana Tanaka or Youbiseiakikana Tanaka, "Kid" could refer to Ryogo Kaburaki or Hokuto.
One example actually does exist, though it is a minor one. Takeshi Kurenari is the name of the main character, and shares his given name with the father of another character (Coco Yagami), although Takeshi Yagami is only mentioned in dialogue and never appears onscreen.
Hakkar (the soulflayer, a serpentine troll god) and Hakkar (the houndmaster, a demon leader) in the Warcraft universe. Chris Metzen, the guy in charge of creative development, later apologized.
Hunters infamously subverts the "Only one name a player" rule, by the fact that no one limits what their pet's names are so a Hunter named "Legolass" could cheating Pv P targetting macros by naming his pets "Legolass", "Legolass" and "Legolass".
Legion Commander Tyralion is a mostly forgettable minor NPC from the second expansion, except for his name, which is almost exactly the same as General Turalyon, one of the Alliance's greatest heroes, who has been missing since the second war. It seems unlikely that the similarity was accidental, but it hasn't been addressed at all.
Anduin Wrynn, crown prince of Stormwind, was named after sir Anduin Lothar, a hero of the First and Second Wars.
Lampshaded in a Winterspring quest. You are sent to kill an owl named Hell-Hoot. It turns out the owl used to be named Deathwing, but once they found out Deathwing was already taken, they had to rename the owl.
Lampshaded again in Vale of Eternal Blossoms. You are sent to kill a wolf named Cracklemaw, so that the name can be used for something else.
Averted in regards to High General Abbendis. While his daughter, Brigitte Abbendis, also holds the rank of High General, he only appears in the manga and the comics.
In Touhou, there are two rabbits with the same surname, Reisen Udongein Inaba (イナバ Inaba) and Inaba Tewi (因幡 Inaba). This is lampshaded in the spin-off comic Inaba of the Moon and Inaba of the Earth.
When the Watatsuki sisters shelter a moon rabbit who went to Earth, they rename her Rei'sen (レイセン) because they were too lazy to learn her real name and intentionally borrow the name of their former pet who also ran away to Earth, our Reisen (鈴仙).
Kaenbyou Rin (燐), the boss from Subterranean Animism shares name with a Dummied Out player character of Embodiment of Scarlet Devil, Satsuki Rin (麟).
The Reimu (靈夢) of the PC-98 era is spelled differently from the Reimu (霊夢) of the Windows era, even though both kanji actually mean the same thing. Fans used to playfully speculate that they were different characters, given the ambiguous PC-98 Retcon.
Almost every Final Fantasy game has a character named "Cid". While the individual Cids that do not co-exist with other Cid in their own worlds are most likely something belonging to some other trope entirely, Final Fantasy XII embraced this one by including 2 Cids: Al-Cid Magrace and Professor Cidolfus Demen Bunasa, Al-Cid and Cid for short respectively. As if that alone wasn't enough, in Final Fantasy Tactics A2, Al-Cid makes a return, only to be in the same clan as an important character named Cid. That makes three Cids in the same Universe.
Although a better example would be in Final Fantasy IV where you have the bard Edward Chris von Muir, who is the Prince of Damcyan. Later on you, recruit the ninja Edward Geraldine, who goes by the alias of Edge. Did we mention he's the prince of Eblan? And then later they are both kings in the sequel. Now, if only there was a character named Ed, we could have a Ed, Edge, and Edward party... Played straight in the Japanese versions where Edward is named Gilbert.
It may also be the main reason why Breath of Fire Ryu never appeared in any Capcom crossover. Despite Capcom showing some interest to test some waters with the series, there's no way that Ryu can compete with the other Ryu on popularity.
The Street Fighter series itself has a "Juli" from Street Fighter Alpha 3 (whose real name is "Julia") and a "Juri" from Super Street Fighter IV. The former's name was even misspelled "Juri" in SVC Chaos.
Then there's Mike from Street Fighter I and the boxer from Street Fighter II, whose original name was Mike Bison (officially abbreviated to M. Bison). Since they're both black boxers with roughly similar designs, this has led to speculation as to whether they're the same character or not.
This is the case in the original Backyard Baseball and Backyard Soccer. After the pros first appear in the series, the trope is averted.
The Paradox Interactive games Crusader Kings and Europa Universalis: Rome have Loads and Loads of Characters and only so many names in the random generator's database; justified, as medieval Europe and (especially) Ancient Rome averted this trope. Crusader Kings II even inverts the trope, as children have a high chance of specifically inheriting their names from their parents or grandparents (rather than simply getting the same name by chance from the database).
There have been several characters named "Fado" in the series. The only thing they have in common is living in a forest. Two of them are Kokiri, albeit from seperate games and centuries apart. It's often assumed Fado from Wind Waker is a Development Gag to Fado from Ocarina Of Time.
Twilight Princess has a swordsman and resistance member called Rusl, while Spirit Tracks has the leader of the Hyrule Castle guards called Russell.
Additionally every female born into the royal family has to be named Zelda, yes every single one. In-series the reason is that this tradition started in memory of a prince's sister who was cursed and fell into a deep sleep that lastee centuries (if not millenia). The only one not named "Zelda" is the one from The Legend of Zelda: The Wind Waker, who is named "Tetra" due to circumstances (though she is called "Zelda" a few times).
(The) Link(s) himself/themselves may count, although not at the same time as one another unless he got ahold of the Four Sword. No Link is immortal, but another one is always born at the right time. In universe, they are referred to by specific titles instead of by name when there is a Continuity Nod. You'd think Ganondorf would seek out and destroy any guy named Link before they became a threat by now...
Strongly averted in the Silent Hill series, reflecting the unreality of this trope. There are many characters with the same given names, and even a few with the same surnames, that are not related to each other. To name a few:
There's James Sunderland (the protagonist of 2), James Wheeler (a sidekick in Homecoming), and Jimmy Stone (Walter's first victim from The Room).
Apparently, Frank is a fashionable name for fathers, since all three bearing that name are daddies: Sunderland (Henry's superintendent and James' father from The Room), Anderson (Emilie's papa from Silent Hill: Arcade), and Coleridge (Anne's father from Downpour).
There's George Rosten (from The Room), George...just George (from Arcade), and George Sewell (from Downpour).
Two Bobbies: Randolph (Walter's second victim from The Room) and Hicks (the DJ dude from Downpour).
Also Mary Shepherd-Sunderland and Maria (both from 2) and Anne Marie Cunningham (from Downpour). The former two are explained below.
Michelle Anderson (Emilie's deceased mom from Arcade) and Michelle Valdez (Cheryl's high schoolmate from Shattered Memories).
Though it might be nitpicking, but "Harry" is actually a form of "Henry" (the former is what happens when you slur the pronunciation of the latter). There's Harry Mason in 1 and Henry Townshend in The Room. And yes, both of them are the main protagonists of their respective games.
The protagonist of Homecoming is Alex Shepherd, whose family is practically a nobility in Silent Hill's neighboring town, Shepherd's Glen. In 2, James' wife, Mary, also has the maiden name "Shepherd" (her surname is hyphenated with James', e.g. Shepherd-Sunderland). It's unknown if they're related, but what we do know is that both are very, very, very important and very, very very insane.
Lisa Garland from 1 and Steve Garland from The Room. They're unrelated.
Becomes a plot point in 2. There are "Mary", James' deceased wife, and "Maria", who is the basically the former but with blonde hair, blue eyes, and a Stripperriffic attire. Yet James, who spends most of his time in Silent Hill with Maria, doesn't seem to recognize the resemblance, let alone the name. That's because Maria is a projection of what James wanted Mary to be: a sensual and energetic woman, rather than the homely and sickly woman that Mary was.
There are quite a few examples of characters in the Fallout series sharing names. For example, Whiskey Bob in Klamath and Herbert Bob the tree.
Also, Vault 108 in Fallout 3 is populated entirely by Garys.
Fallout 3 and Fallout: New Vegas have multiple characters that share the same name. This is never pointed out in dialogue, and confusion is generally avoided due to some of the characters only appearing in the backstory or being known on a Last Name Basis.
Final Fantasy X averts this trope with party member Wakka and semi-important NPC O'aka XXIII. It's so bad that, in the Blitzball Tournament plot point, you'd swear that the crowd was calling for that middle-aged shopkeeper you keep running into.
Somewhat also referenced with Tidus's line, "It didn't even occur to me to think that the Auron Yuna was talking about... and the one I knew from Zanarkand could be two different people. I don't know why, but I knew it was the same guy. I knew it was the same Auron."
Averted with Captain John Price and Sergeant (later Captain) John "Soap" MacTavish in Call of Duty 4: Modern Warfare and its sequel, although the latter's first name was never given in-game until MW3.
Several of the characters from Modern Warfare shared surnames with characters from the original Call of Duty series. In turn, some of these were named after the developers. There are also a few randomly-named Marines in Call of Duty 4 that share names with each other.
In X-COM, the names of your squad members are randomly generated each time you play, and can be customized. In the demo version, however, the names remain static. And in the demo version squad, you have Manfred Geisler and Manfred Unger.
Averted in No More Heroes with three characters named Jeane: Travis's long lost love, his cat (probably named after the former), and a little girl in the real ending.
Dead Rising. In an entire packed mall hit by the Zombie Apocalypse that it was being used as a shelter from, none of the survivors happen to have the same first name.
One of the poker players is named Jessica, sharing the same name as one of the main characters in Dead Rising 1.
John Boog, Johnny James, and Jonathan Kilpatrick, who also goes by the nickname Johnny Pipes.
Left hand Lance and Lance Pennington.
Andy Talbat and Randy Tugman
Kris Bookmiller and Kristin Harris
Hell, One of the main characters, Raymond Sullivan, shares a name with Ray Teller. But this is justified, since Raymond Sullivan is reffered to as "Sullivan" in every instance.
Utterly averted in The Sims 2, especially in Pleasantview, where there are two Brandis (Broke, a playable, and LeTourneau, a Townie), two Townies named Orlando (Centowski and Bertino), two named Amin (Bear and Sims) and two Townies with the exact same full name: Ivy Copur. This is because all Townies and NPCs have names generated from two relatively small lists.
The Total Extreme Wrestling series has Jack Bruce and Jack Giedroyc on their roster.
Averted in Hinatabokko, where both the player and another character are both named Natsuki. It doesn't help that the protagonist has no sprite, meaning that sometimes the only way to tell the Natsukis apart is the context and the fact that the protagonist-Natsuki has no voice.
While it never becomes an issue in-canon, when discussing Ghost Trick you may have to specify whether you meant Sissel the protagonist/cat or Sissel the dead fiancee of Yomiel, who goes on to live in the new timeline.
The Mass Effect series normally follows this rule, but...
There have been four (and counting) Jacobs in the series; Mass Effect 2 party member Jacob Taylor, the guy on life support from the "Lost Freighter" sidequest in the first game, Rebekah Petrovsky's late husband, and her unborn son, although the latter is more often called "Jake". One of BioWare's writers must like the name....
Invoked in Mass Effect 3 with James Vega, who was originally named James Sanders during development. The name was changed to avoid people thinking he was related to Expanded Universe character Kahlee Sanders. This is referenced in-game if you take James to the Grissom Academy mission and meet Kahlee—he mentions that his father had the last name Sanders ("no relation"). James' given name is the same as a "James" who served under Ashley Williams, whom she mentions in an e-mail to her sister. Ashley calls the party member "Vega".
Diana, the mother of Nef, one of Morinth's victims, shares a name with Diana Allers, the Alliance war correspondent from Mass Effect 3 .
The Mass Effect series actually breaks this rule quite a bit. You've got David Anderson and David Archer, Gavin Hossle and Gavin Archer, Elias Keeler and Elias Kelham, and, of course, Steven Hackett and Steve Cortez.
In 1 there's a gun called the Reaper. No relation to what the Big Bad is. It's not even a particularly quality gun. A poetic title for one of the assignments, "Old, Unhappy, Far-Off Things" is from a poem called "The Solitary Reaper", which again has no relation. Unless you really stretch and go with the Wild Mass Guessing that batarians have been Reaper-influenced for decades and the barbarous treatment they use on captives reflects that.
An easy-to-miss correlation of names comes with two very minor characters, Jona'Hazt (only ever mentioned) and Jona Sederis.
In Epic Mickey, there are two extras named Ian. No attention is brought to this, though the game distinguishes them by referring to the pirate as "One Eyed Ian" and the ghost simply as "Ian."
Catherine has the protagonist, Vincent, caught in a love triangle between his long-time girlfriend called Katherine and a gorgeous young woman he met in a bar called Catherine. Coincidentally, the game has only one Steve.
Shining Force games love to recycle names. Not just common names like Max or Arthur, but also more oddball ones like Hig(g)insnote Higgins (two "Gs") is a Paladin in Shining Force II, while Higins (one "G") is a Ninja in Shining Force Gaiden II.
Tales of Symphonia has an interesting example of a by-product of this: While Raine claims that Mithos is a common male name the "Mithos is THE Mithos" revelation is pretty transparent because you never actually meet anyone with that name other than him (and judging by Genis's reaction, the party didn't "off screen" either). A similar example is when Zelos becomes suspicious of Regal's identity and admits that he's wondering if he's "that Regal or not", he is, and you never meet anyone else with that name.
The original Double Dragon has Billy Lee (the Player 1 character), Williams (an enemy mook) and Willy (the final boss, often nicknamed "Machine Gun Willy" to avoid confusion). All of them being variants of the name "William" (although "Williams" is technically a surname).
While the first game featured a Giant Mook named Abobo, Double Dragon II: The Revenge featured two other ones named Bolo and Abore, although the former looks exactly like Abobo, but with long hair (to the point that he is even listed as "Abobo" in the Mega Drive version).
The arcade version of Double Dragon 3 has a "Jim" as the first boss (not to be confused with Jimmy Lee, one of the heroes) and a "Li" as the second boss (who is unrelated to the Lee Brothers, despite being a Bruce Lee Clone like them). Then there's "Sonny" (the third Lee brother) and "Sunny" (the second Urquidez brother), two different characters with similar names.
As mentioned in the pro wrestling section, WCW had several wrestlers named Rick. Their 1994 Super NES game Super Brawl Wrestling featured four of them (Flair, Steiner, Steamboat, and Rude). The strange thing about this is that it makes the game hard to date as the four men were never in the promotion at the same time. note . Steiner debuted in the company in 86 and left for the WWF in 92; he did not return until 96. Steamboat left of the WWF in 84; he returned briefly in 89, and permanently in November 91, staying until he retired in 94. Rude left for the WWF in 87 and returned in October 91; he stayed in the company until 1994. Flair left for the WWF in June 91 and returned in 93.
The Dragon Age franchise has two Templars named Otto. Ser Otto in Origins is a well-meaning blind man investigating a haunting in the alienage. Ser Otto Alrik in Dragon Age II dreams of magically lobotomizing every mage in Thedas, partly so he can sexually exploit them.
Origins has both an offscreen town named Oswin and a minor character named Oswyn.
Mario & Luigi: Dream Team has an interesting example of this in the Battle Ring (with the same character being fought in different battles). There's Bowser X... who's fought alongside Antasma X, Bowser X (who's the X version of giant Bowser)... and they're both named the same as the secret Bonus Boss from the last game in the series. This can make it pretty confusing if someone describes one as That One Boss or something similar without saying what they're referring to.
In Assassin's Creed IV: Black Flag, there are two Edwards: Edward Teach, though he goes by Thatch and is better known as Blackbeard, and Edward Kenway, the playable ancestor.
Super Smash Bros. Melee has a playable character from Fire Emblem: Binding Blade named Roy, and Super Smash Bros. for 3DS/Wii U has a playable character from Super Mario Bros. who is also named Roy. Also, the Colonel, who appears as a Non-Player Character in Super Smash Bros. Brawl, is named Roy Campbell. The Fire Emblem Roy returns as a downloadable fighter in 3DS/Wii U, making them the first games in the Smash series to have two playable characters with the same name (ignoring alternate forms of characters or Link's Legacy Character status, but even in those cases the game picks descriptors such as "Dr. Mario" and "Zero Suit Samus". The two Roys are both just "Roy".)
Super Mario Bros almost averts this with Luigi and Ludwig von Koopa. Both "Luigi" and "Ludwig" are variations of the name "Louis".
The series in general has certain enemies that share the same name despite being wildly different. For example, "Big Bertha" can refer to both a rare fish enemy from Super Mario Bros. 3 or a rare cannon enemy in Super Mario RPG, a "Fuzzy" can refer to the furry, black creatures introduced in Super Mario World or the floating, white creatures that cause dizziness in Yoshi's Island among others.
Although it's changed now, and wasn't present in Japanese, there also used to be two different enemies named "Goomba": The kind eveyrone's familiar with, and the round ones from Super Mario World. Eventually, the latter was changed to "Galoomba".
Slightly parodied in Super Mario RPG. Your team gets to Nimbus Land, full of cloud-people. You are introduced to the long-lost-but-suddenly-returned Prince Mallow, who is... a giant bird. Your teammate Mallow, who is a cloud-person long separated from his parents, thinks the name similarity is a coincidence. (It's not, of course; Bird Mallow is an impostor named Dodo.)
Two different protagonists have the Canon Name "Mark": The male A Wonderful Life protagonist and the male Island of Happiness protagonist.
Anna is Basil's wife in Harvest Moon Friends Of Mineral Town. The game also has an "Ann", who is Doug's daughter and a bachelorette. Ann, as mentioned above, also has a grandmother named "Ann" but this isn't referenced outside of 64 and might not be canon in Friends Of Mineral Town, due to the games being from Alternate Universes.
There's a minor character named "Louis" in Back To Nature and a major one named "Louis" in Save The Homeland.
In the Japanese version of Harvest Moon: Island of Happiness a character is named "Lilly" but internationally she was renamed "Lanna". Alternatively, from the same game the character known as "Suiran" was renamed "Lily".
The Gameboy games have a character named "Kate" while Save The Homeland has a bachelorette named "Katie".
The Papa Louie Arcade series of time management games currently has 90+ customers who can visit your fast food establishments, and no two have the same name. (Although a few have similar names, such as Peggy/Penny and Mindy/Mandi.) Given the limited supply of distinctive reasonably common names, this has resulted in characters named something like Cletus or Xandra.
9 Elefants has police inspectors Lequais and Lequais. Given that they look exactly alike, they're either twins or a deliberate joke.
Nasuverse, in particular Tsukihime and especially Melty Blood has a weird case of this: We have three Akihas in Melty Blood, two Arcueids (three if we consider her original form Archetype Earth), and a whopping four Shikis in the entire Nasuverse. Here's the thing: The different Akihas are just different versions of the exact same character, Akiha Tohno, one normal, one normal but in alternate outfit, one her Super-Powered Evil Side of sorts. With Arcueid, one is her normal form, the other is her Superpowered Evil SideEnemy Without... something, and then there's Archetype Earth. The Shikis are slightly more complicated: Two of them, Shiki Tohno and Shiki Nanaya, are the same person, the latter being, again, Super-Powered Evil Side. Then SHIKI (the all caps is important) is his evil brother of sort. The last one is Shiki Ryougi, who is instead from Kara no Kyoukai verse, different from Tsukihime (although she a Guest Fighter in Melty Blood). The only similarity the four Shikis has is that they have some form of Mystic Eye.
Time Crisis features two Giorgios: Giorgio Zott, a general of the Zagorias Federation (and Big Bad of 3) and Giorgio Bruno, an Italian VSSE agent (and Player Character of 4). They never appear in the same game.
Tekken features a meta example. Resident taekwondo practitioner Hwoarang has a name that's nigh unpronounceable to many people, even the in-game announcer himself. To avoid misspelling the name, most players just dub him "Bob", an abbreviation of Boy on Bike. It becomes confusing when an actual character called Bob is introduced in Tekken 6, apparently as a jab at serious players who can't spell Hwoarang's name properly.
It may not be obvious, but there's Michelle and Miguel. Both are different forms of the same name (Michael); the former is the French feminine form, while the latter is the Spanish masculine form.
Defied in Megadimension Neptunia VII, which has two characters not only named Neptune, but they look and act nearly identical - in fact they're the same person from different dimensions, with the only major difference being that one is visibly older than the other. The other characters in-story occasionally trip over themselves when trying to address one of them specifically, usually resorting to calling the newcomer "Big" or "Older Neptune". Even the game menus struggle a little, calling her "Neptune (Older)" when they can't use a picture.
Animal Crossing has a few accidentally similar named characters due to having Loads and Loads of Characters. For example, the English games have "Bones" the dog and "Boone" the gorilla. Due to the inevitable Dub Name Change, some characters have the exact same name in some languages, but never two characters that appear in the same game.