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Kain from Final Fantasy IV is a good candidate for Trope Codifier: He's Cecil's childhood friend, his most trusted comrade and right-hand ally, and also his greatest rival, primarily in his competition for Rosa's affections. He's the dark and conflicted Anti-Hero to Cecil's noble and righteous Cape, and during a stint where he's Brainwashed and Crazy he acts as Golbez'sDragon. In The After Yearshe gets appointed the Captain of Baron's airship fleet, and with Cecil as king, Kain is his general now. And here's the real kicker—not only is Kain's weapon of choice spears and lances, but his job class is Dragoon. In other games in the series, the Dragoon job is called "Lancer," meaning not only is Kain the Lancer, he's a Lancer to boot.
Barret Wallace from Final Fantasy VII is a unique mix of Big Guy and Lancer, with bonus Token Minority points thrown in. He even founded leads the Well-Intentioned Extremist organization you start off as part of, and sometimes seems a little too ready to think of himself as The Hero early on. Ironically, when Cloud leaves the party after being incapacitated by Mako poisoning, it is expected that Barret will lead the party. Instead, he tells Cid, who appropriately wields a lance, that he's the new leader.
Final Fantasy IX rotates this role a bit during the game: it starts as Blank, but he doesn't last very long in the party. Then Steiner takes over the role, before Amarant firmly and truely takes on every trope associated with Lancerdom. Amarant is Zidane's psuedo-rival, and has a lot of Arrogant Kung-Fu Guy issues that get solved during the course of the game. Oddly enough, the one character that actually uses lances, Freya, never actually takes on this role at any point in the game.
In Final Fantasy X, Jecht qualifies as the lancer to his original team members Braska and Auron. As for the main party, Yuna is The Hero with Tidus as her Lancer. Another interpretation has Titus as the hero, Yuna as The Chick, and Wakka as the Lancer. Or even another with Yuna as the hero, Kimahri Ronso as the Lancer, and Tidus as a modified version of the Chick.
In Final Fantasy XII, just as Ashe is the series most standard hero, Balthier is the most standard lancer.
He did claim to be 'the leading man,' but he matches more with Lancer tropes then the rest of the characters. Fran lampshades this when she replies to his "I am the leading man" by saying "I think you are more of a supporting role." He scoffs, and tells her to stop being silly.
Final Fantasy XIII has Lightning backed by Sazh. Being older he may very well have more military experience, but he has less drive as a leader (stepping down from a more active piloting career in order to take care of his son).
Fire Emblem 4: Prince Quan is both the best friend and The Lancer for Lord Sigurd in the first part of the game. He also has his Lancer in the form of his protege Finn. In the second part of the game, Ayra's son Ulster is The Lancer to Sigurd's son Seliph. And so is Leif.
In Fire Emblem 8: The Paladin Seth is The Lancer to either Eirika or Ephraim, depending on the route you take. Innes fits more as Ephraim's Rival than Lancer. Considering Gerik and his mercenaries, Marisa the Crimson Flash fits as his Lancer since she's more of an Action Girl than Tethys, the Team Mom. In the case of Joshua, either Gerik, Marisa or Natasha (in a more serious, White Magician Girl-y way) cane become his Lancers through supports as he rebuilds Jehanna ) Rennac is The Lancer in L'Arachel's Power Trio.
In Halo 3, the Arbiter plays the role of Lancer to the Master Chief. Johnson even more so
Proto Man (Blues) often fills in this role in the original Mega Man games. Zero in the X series takes it a little bit further, as his antisocial nature has led to more than one physical fight with X. Dex nails the Lancer role in the Battle Network games.
Dex tries, but he comes off as being the would-be hero that manages to do something right...almost never. Protoman and Chaud claim the role of Lancer all over again, being a far more serious threat to both the enemy and the hero.
Dex might actually be an inversion. He has nothing but leadership abilities. He's a fantastic leader and motivator, but lacks the competence to back it up, which is all Lan's. This would probably be why he ended up mayor of ACDC Town in the series ending.
Though they're technically on opposite sides, the prosecutors from the Ace Attorney series often become closer to The Lancer after a few cases against the main character. Miles Edgeworth serves as more of a permanent Lancer in the story, helping the protagonist out in every game they appear together.
In Tales of Symphonia's initial Five-Man Band, Genis, Lloyd's best friend, plays the role of the more smart and cynical Lancer to Lloyd's idealistic Idiot Hero. Zelos, who joins later, also takes up the Lancer role.
Tales of Vesperia is what happens when you give The Lancer his own game. Yuri is Chaotic Good to the core, unafraid of breaking the law to do the right thing, and frequently gets into arguments with his best friend and rival; Flynn, who takes on the role of a Supporting Leader for much of the game. Yuri himself gets his own, "proper" Lancer in the form of Karol; who is much more cautious and cowardly than Yuri is, but has a more idealistic sense of right and wrong and ultimately develops into a brave leader while Yuri continues to fight in the shadows of other people. Judith, being an extremeBlood Knight, is more of The Big Girl with sprinklings of Lancer traits. She's too similar to Yuri in personality and moral outlook to qualify fully, however.
When Riku is on his own in Chain of Memories, Mickey becomes his Lancer, becoming Riku's support and balancing Riku's darkness and cynicism with his upbeat personality and light.
Axel forms this for Roxas in Organization XIII as well.
Junpei Iori, of Persona 3. Eager to prove himself, bitter about the Protagonist being chosen to lead the team over him, brash, loud, poor grades, and a girlchaser.
And in FES, where Aegis is the Protagonist, Yukari acts as the Lancer to her.
Yosuke is the Lancer in Persona 4, oh so very much. Due to the Protagonist being both The Stoic and a Heroic Mime (aside from battle cries and text speech), Yosuke is much more talkative and chipper, with a little Deadpan Snarker tossed in. While he's very willing to have the Protagonist take over as leader during the early parts of the storyline, his final Social Link scene reveals that he had been a little jealous of the Protagonist's comptetence, and starts a friendly brawl between the two to knock said impulses out of him.
Disgaea: Hour of Darkness: Etna, vassal of negotiable loyalty to demon prince Laharl. Being his go-to girl, and the one who cheerfully tells him she will kill him and take over if he doesn't prove himself worthy of being the overlord. Her starting weapon also happens to be a lance. Rozalin from the second game (with elements of The Chick later), Almaz from the third, and Fenrich from the fourth also qualify.
Lin from Advance Wars: Dark Conflict/Days of Ruin. Possibly combination Smart Guy/Lancer, but definitely a lancer.
Almost every main character from the numerous chapters of Live A Live has a Lancer to go along with him or her. The most clear example, however, is Straybow, who is both a rival to the chapter's main character Orsted and eventually that chapter's final boss after his Face-Heel Turn.
Grandia II: Millenia is the Lancer and also the Veronica to Ryudo.
Fate/stay night has a character called 'Lancer', who also fits this trope fairly well; not only is he amongst the most well-rounded of all the Servants (but isn't a protagonist like Saber) but he also plays the role to the hilt when he joins up with the heroes late in Unlimited Blade Works.
Though for a large portion of the Novel he's an Antagonist. More fitting for the role might be Archer and/or Rin. Both are definitely snarky (though Shirou can be snarky, it's usually only internal monologues), in addition to being cynical and realist respectively to Shirou and Saber's idealist attitudes.
Deugan, from the Video Game/MARDEK Flash game series, is much more level-headed, sensible, and hardworking than the titular hero.
As such, he serves as the tutorial to introduce the reactions battle system.
In Mass Effect 1, Shepard has Ashley and Kaidan, the ones with the most dialogue among the crewmates. And as Shepard's character is fluid, they can fill the role of different Lancer types.
In Mass Effect 2, Miranda Lawson is the official lieutenant to Shepard, but Garrus actively serves as Shepard's de-facto Lancer. During the endgame, there are points where you need to split the squad in two and pick a second leader - the three good choices are Miranda, Garrus or ex-marine Jacob. Picking anyone else will end badly.
In Mass Effect 3, either Garrus (if he's still alive by this time) or the Virmire Survivor counts as this, though the former counts a bit more, having been by Shepard's side for all three games. This is particularly solidified in the last conversation Shepard has with him, where they state that "There's no Shepard without Vakarian".
Dragon Age: Origins: Alistair is very much your cheerful, goofy Lancer. Morrigan can have elements of this as well.
For Dragon Age II, Varric is Hawke's lancer as well as the sibling that survives the escape from Lothering. He's also the only character who will never leave their side whereas other party members have a chance to either die or leave Hawke. Aveline also serves this role as Hawke's first ally who stays by their side for the rest of the game.
Knights of the Old Republic has Carth in the first game and Atton in the second as default, though given the size of your party in both cases other characters might fill the role instead.
Indeed, should one fall to the dark side, you could make the case that Bastila becomes this.
Canderous could be seen as one in general for the initial duology, given how he's the only non-droid character to be a party member in each game, and his darker character aspects can serve as a contrast to the conduct of canon light-side players.
Neverwinter Nights limits your party size to one or two at a time, but all of the possible party members can be lancers.
Neverwinter Nights 2 has a very large party by the end, but the characters most likely to fit as the Lancer are Casavir, Bishop, Sand, and Khelgar.
Black Rose is this to Kite in .Hack. While he is clearly the Hero, she comes on almost all important missions with him and is almost equally famous in the setting. Her Tsundere personality foils Kites at time. She's not as well due to the character class she plays.
Matt Horner from StarCraft II is this to Jim Raynor, an excellent example of the more-traditionally heroic character on a less-traditionally heroic team
In Dark Dawn, Karis and Tyrell trade the role of Matthew's Lancer between themselves until Amiti arrives and takes it over. In later parts of the game, it could be argued that Matthew himself is Sveta's Lancer.
Digital Devil Saga: Heat is definitely the Lancer for the Embryon. While the Hero, Serph, is calm and Level-Headed, Heat is reckless and quick-tempered. Serph is Ice element, Heat is Fire. He is the only member to fully embrace his Atma power. Oh, and he pulls a Face-Heel Turn in the sequel, and dies shortly after..
In most Touhou fanworks, Kirisame Marisa plays this role for Hakurei Reimu. Marisa is the hard-working Badass Normal (or as normal you can be in a world of overpowered girls with magical powers) while Reimu is the lazy genius, and Marisa tends to have her own agenda for solving incidents, while Reimu just wants to get it over with since its her job. This isn't really played up in the games (except for perhaps Imperishable Night, where they face off against each other) because according to the storyline, the chosen character is the only one that actually goes out and solves the incident.
The Orion Conspiracy has the engineer Meyer put in this role for The Hero Devlin McCormack. Meyer loves to cuss. He was a soldier in the Corporation War and is more cynical about it than Devlin. Meyer shows how Badass he is by fighting and killing off Captain Shannon and fending off Lowe the xenomorph. Unfortunately, we do not get to see that fight with the xenomorph. He also has a big picture attitude to situations, in contrast to Devlin, who looks at the little details.
Fear Effect. Royce Glas is in this position, and is the opposite of Hana on a number of things.
The Legend of Dragoon starts out with Dart getting his lancer in Lavitz Slambert. The dutiful knight of Basil is in stark contrast to The Loner. Unlike most iterations of the trope, the two get along great and never have any problems with each other. After Lavitz dies, this role is taken up by Rose, who had interaction with both Dart and Lavitz, but it is expanded after he dies.
Street Fighter has Ken Masters to Ryu. Ken's a rich playboy with a flair for the dramatic to contrast The Hero that is Ryu's stoicism and discipline. Other examples could include Guile to Charlie and Yang to Yun.
Rare trio example: Blue Jake, Blue Jay, and Blue Jim in most Angry Birds games.