Superman. Every hero in comic books, at one point or another, has been compared specifically to Superman, either in how he's similar or how he's different. Even in the case of antiheroes and indy comics, as more often than not, the first thing they'll do is take a swipe at the Superman mythos. The entire genre of superhero comics starts with him. And that's why Superman will always be the greatest, most iconic representation of a superhero.
Elizabeth Swann-Turner and Will Turner are the Pirates of the Caribbean version of this. Used loosely, as heroes aren't as pure in her world.
In Star Wars, Luke Skywalker fits this trope so well that Psychology textbooks show a picture of him in reference to the archetype of a hero. In parts of the Star Wars Expanded Universe, variations on "I won't leave you here. I have to save you" are his catchphrase.
Woody from Toy Story. While he does let his jealousy of Buzz get the better of him at one point, he shows off his role as The Hero by trying to correct his mistakes, and he makes the welfare of the whole group a priority.
Bob Parr(AKA Mr.Incredible) from The Incredibles, who is a superhero not only because of his powers, but because he wants to help people, as shown by the way he assists a little old lady when he's working in insurance.
Flik from A Bug's Life, who starts out looking for heros before realizing his own power.
John McClane, of Die Hard, serves as a deconstruction; his dedication to saving the day and Chronic Hero Syndrome destroy his marriage and strain his relationship with his kids, pushing him into cynicism. He only plays the part of the hero because there's no one else to do it.
Kenny very clearly fills the role of The Hero and The Leader, though he isn't the chief protagonist, thus making him the Supporting Leader.
Frodo Baggins and Sam Gamgee both qualify for the role of The Hero in regards to the protagonist swept into adventure, and Tolkien seems to favor Sam for the part, as his journey is closest to that of Bilbo's in The Hobbit.
In the X-Wing Series books, there are always two to three primary protagonists and viewpoint characters. One or two, depending on whether this book is part of Michael Stackpole's run or an Aaron Allston novel - and whichAaron Allston book - is the suboordinate who experiences more Character Development, goes through personal revelations and a personal plotline, gets beat up, and is generally a good person but not quite "pure", often having some dark guilt, flaw, or secret. The other primary protagonist is always Wedge Antilles, who leads, bounces back from setbacks, has a plotline that isn't really all that personal, and is rarely wrong.
'Starfighters of Adumar, which is intensely Wedge-centered and has no other viewpoint characters, is the exception, and although Wedge is severely heroic and an Ace Pilot there too, he's not The Hero to the same extent.
Discworld usually subverts or averts this trope, often favoring the Anti-Hero instead. Carrot Ironfoundersson of the City Watch plays it straight, being physically and morally strong, but he's not the central protagonist.
In Percy Jackson and the Olympians, we're lead to believe that Percy is the hero of the series. The hero is not who we thought he was. Luke Castellan takes up that role instead. However Percy is still The Hero of the series; he's just not the hero of the prophecy.
Alanna of Trebond, who is deliberately a female The Hero in Song of the Lioness. Among other things, she uncovers a plot to usurp the throne, helps Jon improve relations between Tortallans and the Bazhir, and brings a number of Badasses back to the capital for the Final Battle.
Beka Cooper in Provost's Dog reminds her veteran cop partners of the idealistic reasons they joined the force and recruits fellow trainees (and friendly criminals) to help her solve a case that nobody's supposed to really care about.
In Season 9, Faith has become this to some, including Willow, and stands as perhaps the best example since Buffy's name is mud after she did what she had to do and Angel more an obsessed Anti-Hero. Officially she is The Slayer, despite Buffy being Back from the Dead. In universe and out she is treated as one of the nicer characters at the end, when Buffy Took a Level in Jerkass. And she's treated as The Hero over Buffy even before she saves the world.
Noah's Arc: Though not an action-based series, Noah fits in that he has virtually all the non-combat qualities listed above. He's the protagonist, is morally superior (frequently choosing Honor Before Reason), and compared to the rest of the group has a more balanced personality. He's the one who holds the group together, frequently reminding everyone how much they care about each other, and is almost always right in situations where he provides guidance/leadership. Even the wearing red/blue somewhat fits, as there are several scenes where he wears red specifically to make him stand out from the rest of the cast. He's also invariably front and center in any promotional photos and more often than not in scenes where the whole main cast is together.
However, after Lucas leaves in Season 6, Nathan becomes the hero of One Tree Hill.
Revolution: Charlotte "Charlie" Matheson. However, she is too young and inexperienced to be The Leader.
Roswell: Max Evans fits this to a T. His teammates frequently Lampshades it regularly asking him "What do we do now, Max?" even if sometimes they openly criticize him for his "passively watching" instead of taking action sooner, something that doesn't change when he's actually declared the king of his planet.
A partial exception is Tommy, who is originally the Sixth Ranger in the first season, but in the middle of the second season, becomes the leader as the White Ranger. He then stays on as leader in Power Rangers Zeo, but becomes the red ranger then.
The Kamen Rider series are almost always named after The Hero of said series. In the Heisei series, most of these characters tend to be primarily red or blue in their base forms.
Cale'Anon Vatay of Looking for Group is a textbook example. He starts the comic as a "lone and righteous wolf", but quickly accrues of group of fellow adventurers, including the warlock Richard as his Lancer, whom he develops a close - if somewhat dysfunctional — relationship with. He is not the most intelligent of the bunch, clearly failing to recognize evil early on, but often displays quick thinking and good strategizing ability, especially after taking numerous levels in badass. (He is definitely the newest to adventuring of the main characters, having started out the comic with a healthy dose of Wide-Eyed Idealist.) Considering the actions of some of his group members, he can also be seen as an Only Sane Man. He fights with two swords and eventually shacks up with the resident Action Girl.
Neil Sinclair of Survival of the Fittest is arguably the hero of the series. He might not always make the right calls, but he's about the only character who retains his moral high ground throughout the game, and strives ceaselessly to save as many people as possible. He has the distinction of being the only character ever to form an effectual pro-escape group. Which has a good chance to have succeeded, cliffhanger and Pyrrhic Victory notwithstanding; if nothing else, it's the closest the students have ever come to beating the system.
Averted when Church of Red vs. Blue magnanimously declares it doesn't matter if he's the hero. Tucker is swift to inform him that he is nowhere near "hero", and suggests "participant" or "bystander" instead.