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.
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.
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.
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;
Most male Pokémon 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. N from Pokémon Black and White takes after Kaworu of Neon Genesis Evangelion.
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).
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 Shikigami No Shiro 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.
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.
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...
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.
Some are more blatant than others; Bastila is essentially a carbon copy of Aribeth, and Shale is HK-47 but made of rock.