Athrun Zala fills this role in Gundam Seed Destiny, being The Mentor to Decoy Protagonist Shinn, and following the midseason perspective switch, The Lancer to Kira. The story's told from his point of view for most of the series—and even more so in the compilation movies—and its his interactions with the other two that define the show.
Saji Crossroad, during the second season of Gundam 00. The heroes are, of course, Celestial Being. Saji also pilots the support machine for the eponymous mobile suit which acts as the catalyst.
A variation in Soul Eater. Despite being the eponymous character, Soul is actually The Lancer, and the story's protagonist role is taken up mostly by Maka, although Soul is still consistently in-focus.
And then we have Black Star, who merely thinks he's the Hero. He does in fact get to act the part out, as it were, such as his textbookshounen rescue of Kid from the Book of Eibon.
The Power Trio of Arika, Nina and Erstin aren't the real protagonists of the Mai-Otome manga - it's Mashiro's twin brother.
In Rainbow, Mario is the main character despite Sakuragi being The Hero and Big Good. One could also say that Sakuragi is the main character at first until he dies, and the role then goes to Mario.
In Ergo Proxy, Re-l Mayer is the protagonist for the first two episodes, after which the story will shift back and forth between her and Vincent Law, The Heroand eponymous character.
Puella Magi Madoka Magica: Gen Urobuchi has outright stated that, while the series has her name in the title, Madoka is actually meant to be a supporting character, and the true protagonist is Sayaka. This is not entirely true. While Sayaka is the most traditionally heroic character, Madoka remains the primary viewpoint for the majority of the series. It should be noted though, that Homura acts as a very active Deuteragonist.
In Texhnolyze, while the story is focused on Ichise, Onishi and Shinji have greater impact on the story.
Nanoha from Magical Girl Lyrical Nanoha is one of these, when you think about it. All four of the seasons so far have been focused on the characters she's affecting herself - Fate in the first season, the Wolkenritter/Hayate in A's, the Forwards and Vivio in StrikerS and Tohma and Lili in Force - leaving her development somewhat more subdued. And ViVid has her almost exclusively in the mentor role.
Sakuragi from Slam Dunk. He is definitely the main character of the story, with his development becoming more and more important to the plot. However, Rukawa and Akagi fit the hero mold better, as the Team Ace and Captain respectively. They are often the ones who carry the team.
While Keiichi is undeniably The Hero of Higurashi no Naku Koro ni, Rika is the person who experiences the Groundhog Day Loop, and the person trying to figure out why she is always killed in the end of every arc. Keiichi's just the one who is actively trying to do so, and is unaware of the actual protagonist's plight. Usually.
Jun from Rozen Maiden is this to Shinku; he's the master of Shinku (though she treats him like a servant), Hinaichigo (indirectly) and Suiseiseki and in the manga, eventually Souseiseki as well, but he himself is a Non-Action Guy most of the time, though he can provide useful support from the sidelines. Justified, since he's a human child and an unathletic hikikomori, and both the heroes and the antagonists are superpowered dolls.
Koyomi Araragi from Bakemonogatari is the main character and plays a key role in the arcs, but it's often the girls themselves who are the focus and have to solve the problems themselves in the end.
Zenkichi from Medaka Box. He's the primary viewpoint character and male lead, but it's Medaka who acts as The Hero, and converts previous antagonists to allies. He becomes more and more important to the plot, and is also her Morality Chain. The Big Bad of a later arc even lampshades this, stating that he's the type that that's always supporting someone else, never the main focus.
Lucy of Fairy Tail. Of the main cast members, Natsu is definitely The Hero: he's got thepersonality, is the most likely to take action, and is the one most likely to fight the main villain of the arc (the exception are either when another character has a closer association with the villain, or Natsu is so outclassed only the strongest members of his guild can take him). However, Lucy is the one that plot follows the most, meaning she is either the protagonist or at least co-protagonist.
Lucy is a writer, and it's hinted a few times that the novel she's working on is about Fairy Tail. So it's likely that Fairy Tail is her story…about Natsu.
Code Breaker: Sakurakouji Sakura is the viewpoint character of the series. Despite being quite important due to her status as a Rare-Kind, much of the manga focuses around Ogami.
Everybody in Sonic X Season 3, plays this towards Cosmo the Seedrian. As it turns out in the second-to last episode, she was destined to die from birth.
Prior to this, most of the cast, especially Chris usually played this to Sonic, who despite being the main hero, often got the least spotlight and development each episode.
In Digimon Adventure 02, Takeru has a far greater plot-significance than Daisuke, is far more interesting, more familiar, and is the narrator, yet the series keeps thrusting Daisuke at the viewer.
Kagome of Inu Yasha is actually the main character, and view point character, of the series. Despite that, the plot focuses more on Inuyasha.
The Big Bad specifically notes early on, though, that it's Kagome, not Inuyasha, that he has reason to fear.
Jean, from Nadia: The Secret of Blue Water. Once Jean and Nadia join the Nautilus, the plot becomes much more focused on Captain Nemo and his crew. This is especially apparent in the ending, where for the most part it's Nemo and his crew that save the world, while Jean just simply stands by and watches.
Tomoki from Heavens Lost Property sort of fits this; although he's the center of the harem, and it's hinted at that he's The Chosen One, the drama is largely surrounded the angeloids, and the one who's actually trying to solve the mystery of Synapse is Sugata.
Casca from Berserk, although she can also be consider the tritagonist. She's not as important as Guts or Griffith, but is the third most important characters in the story and is even used as an essential plot device, since the whole story is driven by the relationship that the three characters share with one another.
This was the intention in Dragon Ball Z. The original plan was to follow the life of Gohan the same way the series before it followed the life of Goku. Goku was suppose to die and stay dead after the Cell Saga, with the baton off the protagonist of the story being passed on to his son. fans and the editor wasn't having any of that.
Akira Toriyama has even stated that he ultimately felt Gohan didn't work as well as a protagonist.
Tag and Bink are Dead and Tag and Bink Live, short comics that follow the adventures of two bumbling rebels during the events of A New Hope and The Empire Strikes Back. They also turn out to be Jedi Padawans during the events of the prequels.
Jed from the Star Raiders graphic novel. He starts off as one of the three main characters, but halfway through the story he's sidelined into irrelevancy.
Art Spiegelman (or at least his Author Avatar) in Maus as the story follows him and his attempt to record his father's experience throughout the Holocaust. However, the story is clearly about his father Vladek and his Holocaust experience.
By the end of the story, despite their name being in the title, it's pretty apparent that The Avengers in Avengers Vs X-Men are basically there to punch people and provide a "down in the trenches" viewpoint. The actual main characters are Cyclops, Scarlet Witch, and Hope Summers, with input from Emma Frost and, oddly enough, Iron Fist as well.
The Trail Of Cthulhu is a novel that is made up of 5 interlocking stories. Each story has its own protagonist, but Professor Shrewsbury is the hero of the main narrative.
Nick Carraway may be the narrator, but The Great Gatsby is really all about Jay Gatsby.
Beth from the children's book The Best Christmas Pageant Ever and its sequels
Scout from To Kill A Mockingbird. Most people agree that the true hero of the story is her father, Atticus.
Bryan starts out as one of these in the teen series DRAMA!, but by the third book he's become the focus of the story. This is lampshaded repeatedly.
The protagonist of Aimee by Mary Beth Miller is not the eponymous Aimee, in fact the protagonist is not given a name until the last few pages. It's Zoe. She is the girl who was accused of killing Aimee (when in fact Aimee killed herself). The book is all about the protagonist trying to detach herself from the shadow of Aimee's death.
Vin from Mistborn- she's the main POV character, but the story itself centers more on her mentor Kelsier. Subverted when Kelsier is killed near the end of the first book, after which Vin shoulders the role of both protagonist and heroine for the remainder of the trilogy.
At the end of Monstrous Regiment, Polly realises that Joan-of-Arc-equivalent Wazzer is the one everyone will really remember.
The Dickens novel Our Mutual Friend is presented partly through the viewpoint of Mortimer Lightwood. As the family's lawyer Lightwood has a linking position between the hero and heroine, and is also connected to Eugene Wrayburn, but he has little direct impact on the action until fairly late in the story. In the 1990s BBC adaptation, he also functioned as the narrator.
In SkyClan's Destiny, one of the novels in Warrior Cats, Leafstar is the perspective character, however Stick is the main character and the story centers around his struggles with the evil Dodge.
While The Tigers Wife is framed as a story about a doctor delivering medicine to an orphanage at the same time as she's trying to find out some facts about her grandfather's death, the grandfather is really the central figure of the novel.
In A Swiftly Tilting Planet, Charles Wallace goes Within various people from the past, so he essentially witnesses their stories, and only is it explicit that he's even influencing their action. We assume he is, because that's the point of the story, but his action is reduced. Then, when Charles finally reaches 1863, he is Within Matthew, a paralyzed young man in New England... who is having a vision of where the real action is taking place: Vespugia, South America! There is the big fight that the entire book has actually been building up to.
Xenophon is The Hero of Michael Curtis Ford's The Ten Thousand, but the protagonist and narrator is his slave, Themistogenes of Syracuse, a character Ford created for the novel (unlike Xenophon, who was a real person).
Sherlock is told from the point of view of John Watson, at least in the beginning.
Merlin plays with this trope, as it is Merlin's story, and he really does seem to be the Chosen One, but once you step back and look at what he's been chosen for... His entire purpose in life, his reason for existing at all in the threads of Destiny is to protect Arthur. Arthur's destiny is to be the greatest king Albion has ever known. Who's the Chosen One now?
The finale of Ashes to Ashes reveals that both Sam Tyler and Alex Drake are supporting protagonists for Gene Hunt.
While Power Rangers always has the Red Ranger be The Hero, sometimes they're not the one with the biggest connection to the overall plot:
Power Rangers Time Force: Red Ranger Wes may be the focus of the Screw Destiny subplot, but he's still a civilian caught up in a fight that's not strictly his business. It's Pink Ranger Jen who's the official team leader and who has a personal stake, as the Big Bad killed her fiancee. The third subplot is a romance between the two, but it can be considered more Jen's story than Wes' because of the Heartbroken Badass angle.
In Power Rangers SPD, Jack is the Red Ranger, but the story is more about the Blue Ranger, Sky, dealing with his issues and evolving into a worthy team leader. Alternately, Commander Cruger is the show's focus, as he's the team's commanding officer and the one who has a personal rivalry with the Big Bad.
The Vampire Diaries has Stefan. He is the second protagonist of the series with Elena being the main protagonist.
Ultraman Nexus focuses on the life of Komon Kazuki, a member of the Night Raider team. However, he does not transform into the eponymous hero, making him this trope. But he does become Ultraman in the series's finale and thus, ditches this role.
Kamen Rider Hibiki: Asumu is the protagonist, while Hibiki is the main hero and Oni (Kamen Rider) of the show. Word Of God has it that Asumu was originally to have become an Oni himself at the end of the show, but this didn't happen, and even if it had, he still wouldn't have been The Hero for the main run of the story.
Kamen Rider Kabuto: Tendou is The Hero but Kagami is the POV character and main protagonist. Tendou shares more traits in common with a typical secondary/supporting Rider.
It could be argued that this has happened to How I Met Your Mother as the show has progressed and the emotional core of the show has shifted from Ted's romantic interests in Robin to the Beta Couple Marshall and Lily. This has coincided with the Ensemble Darkhorse Barney getting more and more character development to the point where the premise is a bit of a Red Herring.
Boyd Crowder has become this in Justified, so much so that he had almost equal screentime to Raylan in season 4 so far, even though it was several episodes before they saw each other for the first time in the season and that their stories finally intersected. Now they're competing to find Drew Thompson, and solve the seasons Myth Arc.
In Dragon Quest V, unlike in IV and VI, the protagonist cannot equip the Zenithian Equipment; it's actually his son.
Monkey in Enslaved: Odyssey to the West. The narrative revolves around Trip as Monkey supports Trip on her journey home and her quest for revenge of the one responsible for the annihilation of her village. It's Trip that kills the main antagonist, Pyramid.
Enslaved is loosely based on the Chinese novel Journey to the West, in which this still holds true; ostensibly, it's about a priest named Tripitaka traveling westward to retrieve sacred documents. In practice, it's about Sun Wukong the Monkey King and all the awesome shit he does while he's forced to help Tripitaka on his journey.
Locke for most of the World of Balance in Final Fantasy VI, while the story revolves around Terra, Locke is in the hero role. This changes when Celes becomes the acting protagonist in the World of Ruin. She is less of a Supporting Protagonist however until the ending. Here is how this Trope plays with its common counterpart Supporting Leader
Tidus in Final Fantasy X is an interesting case. The whole point of the game, initially, is that the characters are playing supporting roles in Yuna's quest. They, including Tidus, are merely her guardians to protect her, while she is destined to actually defeat the Big Bad. However, Tidus is the game's narrator, and often points out how, "This is my story." Indeed, the very first line of the game is, "Listen to my story." We eventually learn that Yuna defeating the Big Bad would get her killed while it would just come back later, and it's Tidus's destiny to truly kill the thing. Thus, Tidus and Yuna swap being The Hero and Supporting Protagonist multiple times throughout the game: starting with Tidus as the hero, then switching to Yuna, then back to Tidus, and finally ending with Yuna.
In the sequel, Yuna gets full control of the protagonist role. Even when other characters look like they're going to usurp her role as The Hero, Yuna slaps them back down and says "No. This is my story."
Final Fantasy XI has the player character often playing second fiddle to a (usually female) hero NPC in most of its storylines, doing the heavy lifting while the heroines magically appear wherever you go and have most of the interactions with other characters that the player character would have in most single player games.
Vaan is the Supporting Protagonist to Ashe (and possibly Basch) in Final Fantasy XII, though Balthier would have you believe different.
Allegretto of Eternal Sonata, in the same vein as Vaan of Final Fantasy XII, is most definitely this to not one, but two possible protagonists - Polka, a girl from a remote village who is actually the Messianic Archetype catalyst for the Groundhog Day Loop that the world is trapped in, and Chopin, who claims that everything and everyone around him is merely one of his dreams. The latter's appearance in their world is actually destined to end the loop of Polka repeatedly dying/reliving the same seven years over and over. Other than being the player avatar (and even then, that role is switched between him, Polka, and Beat) and acting as Polka's love interest, Allegretto doesn't even do much in the main story itself.
StarCraft is basically about Arcturus Mengsk, Jim Raynor, Sarah Kerrigan, Tassadar, and Zeratul, whereas the PC is just some generic, nameless "magistrate", "cerebrate", or Protoss "executor". Word Of God has retconned that the Executor of Episode III was Artanis, and presumably the Executor of Ep IV was him or his student Selendis (who is Executor in Starcraft II). The other player characters get fleeting references in the expanded universe to confirm that in the current canon they still exist, but their roles are downplayed because, well, they were always little more than viewpoints for the player to see the characters.
World in Conflict has a named PC, Lt. Parker, but the real protagonist of the 2/3 of the game is Capt. Bannon (who receives ALL of the Character Development in the game), while the remaining one third focuses on Webb and Col. Sawyer. Same goes for Lt. Romanov from the Expansion Pack, who plays a secondary role to Capt. Malashenko and their common superiors.
Subverted and played straight in Brütal Legend. Eddie acts like he's one of these and purposely avoids the spotlight, but everyone else knows he's responsible for their success and thank him appropriately.
The main character in the Neverwinter Nights plague campaign is Aribeth, the player is just the lackey that got sent to do stuff for the political powers he sided with.
For reason of having a Heroic Mime protagonist and a strong supporting cast, GLaDOS is the star of Portal, though Chell is the protagonist. You could go the whole game - perhaps even both games - without ever learning her name, or any other reliable fact about her.
Persona: The player character is this in both routes, as the SEBEC route revolves around Maki coming to grips that she created an alternate reality that's trying to overtake the real reality and the Snow Queen route revolves around Yukino's attempts to save Ms. Saeko.
Subverted in Shadow Hearts: From The New World. Shania appears to be the more important character, with Johnny Garland just tagging along... then it becomes clear who, exactly, Lady is, and It's Personal.
The protagonists in the Ar tonelico series are generally secondary to the Reyvateils, especially Croix in Ar Tonelico 2. So much so that he didn't even appear in the Japanese cover art for 2!
Nintendo-owned developer Intelligent Systems did this in some of the few games they made with western players in mind.
In the original Battle Clash, the player controls the gunner of a giant robot known as a "Standing Tank". The actual protagonist is the robot's pilot, who talks to the player directly before each battle. In the sequel, Metal Combat, there's a cheat code that allows the player to have the pilot address them by name.
In the original Advance Wars, the player takes control of an unseen military strategist who is assisted by a Commanding Officer (C.O.) in each battle. This was dropped in the sequels.
Interestingly, the character you make in White Knight Chronicles is almost a non-entity: although you can use any weapon, armor and magic, unlike any other character in the game, your character is entirely incidental to the plot and can, in fact, be left out entirely. The real hero of the story is Leonard.
While the plot of Super Paper Mario certainly incorporates Mario, Peach, Bowser, and Luigi, the main story focuses on the romance of Blumiere and Timpani and in the end they're the ones who save the Multiverse.
A non-RPG Mario example would be in Super Mario Galaxy, where Mario is just there to fly through space as an attempt to save Peach again from Bowser, who wants to take over the galaxy, but this is actually just a subplot. The game is really about a young woman's Tear Jerker tale of her constant wandering through the cosmos with several little star-people as her only friends while lamenting about the loss of her family since her departure.
The Lord of the Rings Online has its central epic quest line, in which you follow along with the characters in the story and run errands for them. So far, every epic "Book" ends with your watching NPCs finish the fight.
This is actually quite common in World of Warcraft. While the player character does his fair share of heroics, most of the major story arcs have another character with a more important role in the story (probably due to the issues having a faceless character who could be of any race from either faction as a major character would cause). For example, Tirion Fordring is the true protagonist of Wrath of the Lich King. The player character is his Lancer.
In Disgaea 2, Adell is clearly the protagonist, but Rozalin is the one who gets all the character development and plot twists, and she is ultimately the one who vanquishes Zenon.
Also, in Disgaea 3'', Almaz may play this role for the actual protagonist, Mao. Although, unlike Disgaea 2, where it's obvious, Almaz and Mao's roles may largely depend on interpretation.
The Rookie in Halo 3: ODST only begins to affect the story in the last two levels: the rest of the game is spent reliving the experiences of the rest of the squad in the six hours the Rookie was unconscious.
Lars in Tekken 6. He may command an entire army, fight waves of soldiers bare-handed and deflect missiles with his wrists, but the Mishima family are the ones doing all the important stuff while Lars runs around punching folks.
The Faceless Protagonist of The PK Girl is a Supporting Protagonist to Laurie in the main plot. Laurie is the focal character, as the Living MacGuffin and the target of the antagonist, and her attempts to get free of ROSA's clutches drive the plot; the PC's just the guy who does the fighting, heavy lifting and rescue work, and otherwise he's along for the ride. If he's chasing any girl besides Laurie (who is romanced through the main plot), he becomes the protagonist of his own Romance Sidequest, but only one Romance Sidequest ties back into the main story in any way after it starts off (Katryn's).
Tact Mayers of Galaxy Angel. Although he's the captain of the Elsior which is a capital ship all the work is done by the angels.
Leo from Zone Of The Enders has a personal journey, but the focus moves more towards the larger conflict and he's ultimately an insect to the villain. He gets the focus on his journey but the true hero is already dead at game start and his journey is just a small part of the much larger story he was sucked into.
One can get this impression from The Legend of Zelda: Spirit Tracks. While other titles in the series focus on Link— who, of course, plays the hero— Spirit Tracks seems to focus more on the character development of Princess Zelda. Appropriate since, barring thatthat one time, this is the first time that she's playable..
A lot of people had the same impression with Link and Midna in Twilight Princess. Even right before the Final Battle, the Big Bad talks directly to Midna and addresses Link like an afterthought.
The various AFGNCAAP player characters of Ace Combat have been this ever since the series steered away from Excuse Plots (around the time of Ace Combat 3: Electrosphere). Nowhere is this more obvious than in Ace Combat Zero, where the entire game is told from the perspective of the enemy aces you shot down and your ex-wingmanwhom you also shoot down. The Narrator even admits in the end that despite telling the whole story, he still has no idea just what kind of person the Demon Lord of the Round Table was.
Ash in Phantom Brave. Marona is the focus of the plot, but Ash is who you directly control during downtime and the story is mainly told from his perspective.
Artyom in Video Game/Metro2033. Most of the time he is merely following someone more experienced and last part of the game is him essentially helping people who know what needs to be done. He himself does not have much of a goal beyond "Get to Polis", after which he starts following people who react to his news.
Most romantic visual novels are more about the romanceable characters (and one 'true path' character in particular) than they are about the player character. In the Bishoujo setup, the male lead is often either a nonentity, a loser, or a jerk, and one of the female leads is the real hero. This tends to carry over into their anime adaptations.
Fate/stay night is both a literal and figurative example: in the Fate route, Shirou is no match for Saber in combat, and instead supports her with projection and, later, mana. Emotionally, it's his job to break through her stoic exterior and make her happy. Either way, Saber ends up the primary focus, and the driving force of that route.
Nine Hours, Nine Persons, Nine Doors: The point of view that the player takes is actually June/Akane of 9 years ago, seeing things through Junpei's eyes. This is a very important plot device and technically makes her the protagonist. Junpei still fills the conventional role of the hero though and once their connection is split at the very end, the perspective of the remaining story alternates between the both of them.
The Exiles of Homestuck have this going for them in their Five-Man Band. WV, the first Exile seen, is the protagonist of the Exiles and gets the most screentime, but in terms of role in the story, he is surpassed by PM, the one who did more things that were directly relevant to the story.
Jackknife from Superjail definitely qualifies-he's one of 4 inmates that are seen from one episode to the next. (the other 2 being the gay couple and Gary and Bird).
The original premise for Avatar The Last Airbender had Sokka playing this role towards Aang. This did not make the final cut though.