Bomberman's sprite from the original NES game is actually the same sprite used for the enemies in the NES port of Lode Runner, which was released a year earlier. Interestingly, if you beat Bomberman, the ending shows Bomberman transforming into the protagonist from Lode Runner, accomplishing his goal of becoming human. The ending says "You have succeeded in helping Bomberman to become a human being. Maybe you can recognize him in another Hudson Soft game", implying that the game was a prequel to Lode Runner all along. Since then the Bomberman character has developed into something completely unrelated to Lode Runner however.
Devilotte of Cyberbots was built as an expy of Doronjo from Yatterman — both being blonde, female comedic mecha villains constantly accompanied by a pair of male lackeys. Lampshaded in Doronjo's ending in Tatsunoko vs. Capcom, where she ends up going after Devilotte for stealing her gimmick.
There is quite a lot of expies in the Contra series:
The final boss in the arcade version of Super Contra, Emperor Devil Gava(A.K.A. The Red Falcon), is based on Mad Emperor Asmodeus, the final boss of another Konami arcade game, Battlantis. Battlantis was directed by Hideyuki Tsujimoto, who was co-programmer in the original arcade version of Contra and later directed Super Contra, as well as Sunset Riders and Mystic Warriors.
In Contra ReBirth, Gava has mandibles, that make him look a bit like a Predalien.
The Aliens are in series, generally are based on those from the Alien movies. In The Final level of the original game, there is Devil Dragon Emperor Java(the big Xenomorph-like head), and Facehuggers. In Super C and Alien Wars, there are enemies, that look like adult Xenomorphs, not to mention the Metal Alien, who looks like a winged one.
A pretty wierd example from Contra: Hard Corps, were there is an expy of an attack, rather than a character. The first form of Colonel Bahamut after fusing with Alien Cell uses an attack that is pretty much the Continuous Energy Bullets attack from Dragon Ball Z. His second form after he loses control over the Alien Cell looks like Slave Beast Taka, A.K.A The Giant Turle boss from Alien Wars and Shattered Soldier.
The fight against The Relic of Moirai fused with the Triumvirate from Shattered Soldier is oddly enough, an expy of the multi-fazed boss fight against Colonel Bahamut. And their first form resembles Super Buu, again from Dragon Ball Z.
Genbei “Jaguar” Yagyu, is obviously based on the historical Samurai Yagyū Jūbei Mitsuyoshi.
She's actualy more similar to Samus Aran, at least in looks, and her gun is based on her Power Suit. Krystal even has an alternate color scheme, were she looks exacly like ZeroSuit Samus.
Harley = Potemkin + Johnny.
He also seems to designed as a fully human version of Brad Fang, from Contra: Hard Corps.
Leviathan = Ky Kiske + Chipp Zanuff + Lance Bean.
He also resembles Deadeye Joe, from the original Contra: Hard Corps. Both have lower parts of their faces obscured by their masks, both are chased by the player, both have Noble Demon tendencies, and both fight against the player character, personally, and inside a Mecha.
He's quite similar to Jin Kisaragi too. Both are sometimes at least a bit crazy, had a deep bond with one of the characters, that was broken(Ragna/Bahamut), and consider themselves kind-off the good guy, at least in the begining, despite being on the definitely wrong side of the conflict. Their faces and hair are also definitely similar.
He is also an equivalent of Lance Bean, who was Bill Rizer's former friend in the old Contra titles, and now enemy in Shattered Soldier. Both have accused their former friend (Bill/Bahamut) for the atrocities they have done (Bill has accidentally wiped out 80% of human population and nearly killed Lance. Bahamut has betrayed Leviathan and the Commonwealth Empire.) before becoming enemies.
Tiberius = Colonel, or Master Contra of Neo Contra + Chief Salamander of Contra Rebirth.
Tiberius Augustus = Justice.
He also resembles in this form, the first two stages of G-Virus mutated William Birkin, especialy with both sharing the overgrown one arm, with a pulsating, giant eye.
Ironically, he also resembles the Triumvirate from Shattered Soldier if you count the Relic of Moirai overwhelming them.
Tiberius Invictus = Chaos (or, if you prefer, Valentine from the final battle of Guilty Gear 2: Overture, or Project C of Neo Contra).
Some of the enemies too. There's one who resembles a Gigafly (from Contra III, Shattered Soldier and Contra 4) that tries to "kidnap" your character by taking them away to the top of the screen.
Both 573-Tigris and 573-Draconis (Kasuga series in the Japanese version) resemble the Magnus Tank series.
573-Draconis from the end of stage 3, seems to be based on the blue battleship/submarine boss from the begining of the second stage in Contra: Shattered Soldier. It also resembles the TIM Gunboat in Neo Contra.
The Lux Corona resembles a combination of Rocket Ninja Sasaki (from Contra Rebirth) and Great Awakening Robo Big Fuzz.
The transforming black robot from stage 6, looks, and behaves like a combination of Super Power Robot Yokozuna from Contra: Hard Corps/Shattered Soldier, and the Heli-bot from the begining of stage 6 in Shattered Soldier.
Willy'sbodyguard Raymond in Double Dragon Advance is based on the nameless final boss from the second NES game. While the Mysterious Warrior's fighting style from Double Dragon II was called "Gen-Satsu-Ken" (Phantom Murder Fist), Raymond's style is known as "Gen-Setsu-Ken" (Phantom Interception Fist).
Duke, the Big Bad of Super Double Dragon, also resembles the Mysterious Warrior.
The dragon in Dra Koi is an expy of Lala Satalin Deviluke from To Love-Ru in appearance, though her personality is only somewhat similar. They both have long pink hair and a very distinctive hat. In the case of the original, it's a shapeshifting robot. The dragon's hat just happens to look like it.
Nearly all the agents in Elite Beat Agents were designed to be westernized versions of their Japanese counterparts in Ouendan.
While not applying to a Character, the double-barrelled Devestators of Dune II have an expy in all Command & Conquer games to date save for Tiberian Sun, in the form of the Mammoth, Apocalypse and Overlord tanks.
Here's a really weird one. Okay, so there's this major character. They're the only child of a noble family, and they posses a rare but dangerous power. At the beginning of their game, they're kidnapped by the person who will eventually become their love interest and spirited away to an opposing Empire - oddly enough, this Empire seems friendlier to them than their actual homeland. Eventually, the character suffers a huge mental trauma; they witness the destruction of a city, and realize that it was their awesome power that indirectly caused it. Around the same time, they realize that they're not really the noble family's child, but a nearly identical replacement of the real child, and on top of that, they're not even human; they're a different kind of being entirely. They spend the next little while in a combination Heroic RROD / Heroic BSOD, and are rendered both temporarily mute and restricted from battle. Eventually, the character decides to become more independent and make their own decisions, while atoning for their mistakes. The character borrows a knife from their love interest and gives themselves an Important Haircut, and from then on, they return to the party in full force. Now, does this describe Princess Garnet in Final Fantasy IX or Luke fon Fabre in Tales of the Abyss? Aside from their genders, the similarities are uncanny.
Each of the Dickens sleuths in Guilty Party draws direct inspiration from another famous detective character. Dorian "The Commodore" Dickens is Sherlock Holmes, with his vaguely British accent and deerstalker cap. Max Dickens is Sam Spade, with his fedora and trenchcoat. His sister Phoebe, with her FBI badge and habit of being the only sane one, is Agent Scully of The X-Files. Her son Rudy "Kid Riddles" Dickens, the overenthusiastic child detective, is Encyclopedia Brown. On the Dickens-Johnson side of the family, Dorian's sister Charlotte Dickens is a investigative little old lady in the mold of Miss Marple. Her husband, Butch Johnson, is a tall, imposing man in the mold of Shaft (daaaamn right). And their adoptive daughter Ling Ling Dickens-Johnson is a smart, analytical teenaged girl in the mold of Nancy Drew.
Inazuma Eleven GO plays this with the manager trio, Sorano Aoi, Seto Midori, and Yamana Akane are expies to the prequel's Aki Kino, Raimon Natsumi, and Otonoshi Haruna.
The commentator Kakuma Ayumu is this to Kakuma Keita. After all, they're brothers that have a common interest and share the same VA.
White haired half-demon who fights demons using a sword he inherited from his legendary demon father. His brother, similarly white haired and wielding a sword inherited from their father, who fell in love with a human woman before his death. A thousand points for anyone who can identify whether this description is of Inuyasha or Devil May Cry's Dante.
Lololo and Lalala (aka Fololo and Falala) from the Kirby series are based on Lolo and his girlfriend Lala from the Adventures of Lolo series, having almost identical character designs; Lolo and Lala have mouths, while Lololo and Lalala do not (as they are based on Lolo and Lala's sprite artwork, where their mouths are generally Invisible Anatomy).
Louis also has his clothes and background being an almost duplicate of the title character from Shaun of the Dead. Once Louis and the other survivors from the first game were made available in the second game, the resemblance is even more similar once you give Louis a cricket bat.
Malladus from The Legend of Zelda: Spirit Tracks is a blatant one of Ganon from the rest of the series. Demon King? Check. Wants to conquer the world? Check. Possesses the princess? Check. Has an evil second in command who's trying to revive/unseal him? Check. Looks like a giant blue pig/boar creature? Yep. Heck, he's even defeated by Link and Zelda working together and using the Light Arrows, complete with a death involving being stabbed through the forehead with a magical sword. Indeed, he's so much like this you could probably replace him with Ganon and not have to edit the story one jot.
Due to the cast being Identical Grandsons of any similar-named character, technically every Zelda, Link, etc. from a Zelda game that is not explicitly a direct continuation of another is an Expy and not a returning character.
Kyousuke of Little Busters! is clearly based on Yoshino Yuusuke from CLANNAD, both having similar hairstyles, voices, and names, and propensities for inexplicably charismatic speeches about love or friendship or hope in totally mundane situations. However, they're far from the same character - for example, where Yuusuke is always totally serious and stoic, Kyousuke is much more overdramatic and expressive and happy. Most of all, Kyousuke comes across as something of an expansion on Yuusuke's character, as while Yuusuke only ever had a minor role at best in CLANNAD, being mostly a one-off joke, Kyousuke is absolutely integral to the plot of Little Busters! and gets a whole lot more character development.
Lesley, of Ayako Katagiri: they share the same specific personality traits unique to their character, i.e. an obsessive love for painting, and a horrible fear of water which plays an important role in some special Events and dates at swimming locations;
Nefarious has Princess Mayapple, who is pretty much Princess Peach by another name, sharing the same style outfit she has, as well as the same dynamic with Crow that Peach has with Bowser. Albeit, she's a tad bit more snarkier about her frequent kidnappings by him than Peach is.
Teddie's human form on the other hand is an Expy of Ryoji Mochizuki from Persona 3, in personality, personal struggle and partially their eventual role in the story. The biggest difference, however, is that the former manages to avert falling victim to the same fate the later fell to by the end of the game - but just barely.
Rise Kujikawa of Persona 4 is an expy of Lisa Silverman from Persona 2 in everything expect the later's love for Kung Fu (which went to Chie Satonaka instead). They even share the same default Arcana (Lovers) and early concept art of Rise looks like Lisa with a slightly more Asian look. It also helps that their names sound very similar in Japanese (Rise VS Risa).
And then there's Yosuke Hanamura (Persona 4), who starts out as a complete expy of Junpei Iori (Persona 3) to the point that they even have some of the same lines early in the game. (The Artbook has the designer admit that he intentionally designed Yosuke to look more youthful than Junpei because he got annoyed with how much the rest of development team was treating him as essentially "Junpei 2.0".) However, as both of them eventually come into their own in different ways, Yosuke being a complete Expy is ultimately averted.
Most of the male protagonists are expies of the original hero, Red. Ethan, Brendan, and Lucas take after his original design while Hilbert, Nate, and Calem take after his modern one. The latter two are also expies of Hilbert, most obviously with Nate.
Throughout the series, species have tended to repeat themselves as well:
Most infamously, Series Mascot Pikachu has had a new cheerful, circle-cheeked, Fragile Speedster electric rodent just like it in every generation, in order: Pichu, Plusle and Minun, Pachirisu, Emolga, Dedenne.
Every generation except 6 has a small, cute, unobtainable legendary with an even spread of 100 among all stats. In order: Mew, Celebi, Jirachi, Manaphy, Shaymin, and Victini. To further the pattern, all but two, Manaphy and Shaymin, are at least part-Psychic-types.
The earlier routes are known for having a number of recurring patterns in the Com Mons, such as with the Normal Rodentsnote Rattata, Sentret, Zigzagoon, Bidoof, Patrat, Bunnelby and the Normal/Flying Birdsnote Pidgey, Starly, and Pidove along with Spearow, Hoothoot, and Taillow. X and Y has noticed the pattern and subverted it; Bunnelby evolves into Diggersby, a really not cute Normal/Ground type who's a Mighty Glacier rather than a Fragile Speedster, and Fletchling, who at first appears to be the Normal/Flying bird, evolves into Talonflame, a Fire/Flying type who's one of the deadliest non-legendary pokémon in existence.
Black and White was known for completely wiping the pokédex up to that point to fill the region with new species. While this has had different results depending on who you ask, the Roggenrollanote Expy of Geodude, a three-stage rock-type that had the ability Sturdy and had its final stage evolve by trade, Woobatnote A very common bat that confused opponents like Zubat, Audinonote A pink, fluffy Metal Slime that spreads joy and commonly works in medicine, like Chansey, Timburrnote A three-stage fighting-type with very high attack and has the last stage evolve through trade, like Machop, Throh/Sawknote Hitmonlee/Hitmonchan, twin fighting types which looked similar but had different focuses, along with the fact that you could only have one of the two, and Bouffalantnote A normal-type bovine that strongly resembles Tauros with an afro lines seem oddly familiar.
Randy and Andy, the Dragon Twins from River City Ransom, are based on Billy and Jimmy Lee, right down to using their same theme music. The reference was even more blatant in the Japanese version, Downtown Nekketsu Monogatari, where Randy and Andy's Japanese counterparts were originally named Ryūichi and Ryūji Hattori (their names meaning First Dragon and Second Dragon).
In Robopon, Robopon 64 had you play as expies of Cody and Bisco, the hero and his rival from the GBC games.
The titular Serious Sam is pretty much the equally titular Duke Nukem without all the sexual and toilet humor (but still with plenty of cheesy one-liners.) This, plus the fact that the first game came out the same year that 3D Realms announced "Duke Nukem Forever will be done when it's done" could be used to argue that the former is a Spiritual Successor to the latter (especially when Duke Nukem Forever bombed horribly, while Serious Sam 3 fared considerably better.)
Anne Lafitte of Shadow Hearts: From The New World, is basically Anastasia from Covenant .
To say nothing of Lady and Killer, who are basically evil Alice and Yuri.
Both Miko SHMUP Heroines Sayo Yuuki from Castle of Shikigami and Reimu Hakurei from Touhou are said to be based on Sayo-chan/Pocky from Kiki Kaikai/Pocky and Rocky.
Gigadis and Kuu(-chan) from Sorcery Saga are extremely transparent stand-ins for Satan and Carbuncle from the earlier Madou Monogatari titles and Puyo Puyo. We also have stand-ins for Rulue and Schezo, but Pupuru is not intelligent or sarcastic enough to be a proper Arle expy.
Ni No Kuni has Marcassin, who is an absolute dead ringer for Howl. In the English version, he even spends his first few moments on screen hiding his face, complaining about how "hideous" he is—just like Howl does! (This isStudio Ghibli, however, who are known for their Star Systems.)
There's also the Toko class of creatures, who are an obvious Totoro expy, especially Chibi-Totoro.
Alt Eisen -> Vita; her barrier jacket is predominantly red and black (with some white highlights), her armed device is called "Graf Eisen" which, while a hammer, functions as a barrier-piercing Pile Bunker via spending cartridges and also has the power to attack her enemies with tons of iron balls.
Aside from the Hermodr battleship and Zyflud, none of the Balmarian mecha in Shin Super Robot Wars reappear in future SRWs. However, the Zadoc and Cees in Shin are most likely the base designs of the Zechariah and Megillot from Super Robot Wars Alpha.
The multiplying, regenerative qualities of the Machine Cells from Alpha Gaiden are the SRW equivalent of DG Cells.
Each of the original mecha in Super Robot Wars 64 are essentially slightly redesigned and recolored for the ones in Super Robot Wars Advance: Earthgain -> Soulgain; Super Earthgain -> Zweizergain, Virose -> Vysaga; Simurgh Splendid -> Angelg; Soldifar and Ashcleef -> Ash Savior; Svanhild -> Laz Angriff; Rathgrith Custom -> Laz Angriff Ravennote Laz Angriff Raven, however, only appears in Super Robot Wars Original Generation.
Gundam -> Huckebein series; this example is rather infamous, as the entire mech family got bridge'd in 2nd Original Generations after Sunrise complained about the similarities. This resulted in the creation of the Exbein, which is about 99% identical to the old Huckebeins, lacking only the most blatant Gundam design elements.
SolForce from Sword of the Stars is one for EarthForce from Babylon 5. The name and functions are similar, the backstory of SolForce involves a democratic administration being suborned by jingoist militants that eventually get pushed back, just like the other, and the creators have even admitted to being fans of the show.
The Bloodweaver aka He Who Shapes is the most paternal of the Suul'ka and the most adept at biological warfare. The Zuul females under him are constantly in pain and warped in form. Doesn't that sound like Grandpa Nurgle?
The Loa to the spirits in real life Haitian Religion, http://en.wikipedia.org/wiki/Loa. Hardly surpriseing, as most races have some kind of historical analogue and the Lore writer is trained in historical anthropology.
Despite the name, the Zuul are more like the Reavers from Firefly. Ramshackle ships, into abduction, piracy and slaving, have a taste for rape (mental, not physical, which isn't much better) and murder, make lots of use of grappling harpoons and Boarding Parties...
Milla from Tales of Xillia bears similarities to Dhaos, having a mastery of four basic magic elements, and also having a mission to destroy the technology that's disrupting her world's mana. Appropriately, she gets his outfit as a costume.
Dhaos gets a second, villainous Expy in the sequel in the form of Khronos, who possesses all of his signature moves (Tetra Spell, Tetra Assault, Khronos Corridor/Laser), and harbors a similar disdain for humanity. It's likely a nod to the fact that a renamed Dhaos served as the Craymel of Time in Tales of Eternia (Khronos being the prime spirit of time in Xillia's universe).
Tech Romancer, being an homage to mecha anime, has Expies out the wazoo, for both the mechs and their pilots.
Carley from The Walking Dead is an expy of Rebecca Chang from Dead Rising 2. Both women are pistol-toting attractive reporters who wear the same outfits (a white buttoned shirt, black skirt and matching slippers/heels), and they both die very shocking and sudden deaths from being shot in the head.
The Quarter Knights in the original Wild Arms are based on the Sinistrals / Four Mad Gods from the Lufia / Estpolis series.
According to top BioWare writer David Gaider, BW's writers build characters by taking ones from other works and reworking their names and backstories.
Alistair for example was heavily based on Xander from Buffy the Vampire Slayer.note This is why they chose the name Alistair, it's the Scottish form of Alexander.
Vette from Star Wars: The Old Republic is an egregious case; same species (blue Twi'lek), personality, and voice actress as Mission Vao. The main difference is that Vette's "of age" and a romanceable option.
Bioware characters also tend to be expies of each other, often sharing personality types, abilities and backstories. ThisCracked article points out a few.