Kaitou Saint Tail grew feelings for the detective pursuing her, but he was so obsessed with catching Saint Tail that Haneoka Meimi barely registered. In one episode, she gets so frustrated with him that she yells her secret identity in front of the whole class, and his response is "...what was that about Saint Tail?" This gets Meimi so frustrated that she jumps between wanting to give up the secret identity and just wanting to have nothing to do with him. Later, her identity finally begins to register with him, after a magic mirror that shows your True Self displays Meimi instead of Saint Tail.
Light/Kira from Death Note, to the extent that by the end of the series, Kira has abandoned nearly all of the ideals which Light used to stand for.
Also from the manga version, Usagi is shown being confused about which of her three identities (Usagi Tsukino, Sailor Moon, Princess Serenity) is the "real" her.
Princess Tutu is essentially a role assumed by Duck, predating the Secret Identity and granted by Drosselmeyer. While the two are clearly the same person, their behavior is markedly different, and not just because Duck is the worst dancer in the series while Tutu is probably the best.
And add in another layer that Duck is also uncertain if she's really a Bird, a Girl, or a Princess. That's three competiting identities.
Hei in Darker Than Black has two identities, AdorkableNice Guy Li Shenshung, a Chinese exchange student, and the Black Reaper, a remorseless mass-murdering assassin and spy. When he's talking to people as Li, it's easy to tell when someone hits a nerve because his eyes will go so ice-cold that he looks mind-controlled. And when he's the Black Reaper, he wears a whitemask. At the beginning of the series, it seems like the Black Reaper is his true character, but it gradually becomes clear that while neither persona is the real Hei, he's actually closer to Li, but ended up stuck playing a different role due to his Dark and Troubled Past.
Code Geass plays with this trope when it comes to resident Anti-Hero Lelouch: Lelouch Lamperouge is, of course, the civilian identity he adopted to hide from The Empire. Lelouch vi Britannia is his birth identity, which is legally dead. And finally, we have Zero, the over-the-top dark avenger/terrorist/freedom fighter/resistance leader persona. However, the question as to which one is real is largely subverted. Lamperouge is completely made up; however, it is the identity he uses with his friends and sister, seeming to be the most "real" near the end. Vi Britannia is the identity he truly hated, due to his hatred of Britannia, but it was also the one his royal sibling recognized him as. Zero, meanwhile, seems to represent his Large Ham tendencies, as well as his inner hatred and desire for justice. At times, he seems to consider Zero his True Self. Near the finale he seems to come to terms with this and states "I finally know who I really am!" when he kills his parents. He later uses the vi Britannia identity to take over the world and initiate the Zero Requiem, becoming known to the masses by that name. As Emperor Lelouch, he displays traits common to all his personas: Zero's hamminess, vi Britannia's royal bearing, and Lamperouge's (very well hidden) kindness. The debate as to who he really is ended up being so divisive to fans that claims to his survival or death are often attributed to which "identity" has died.
JoJo's Bizarre Adventure: Vinegar Doppio has a rather unclear case of this. Despite his alter ego as Diavolo he isn't aware of it himself but it acts as an actual split personality. It's never revealed which was the original persona though it's implied that Doppio was Diavolo's persona he used to seem inconspicuous before the two personalities split apart.
At one point of the manga version of Cat's Eye, the girls decide to try and draw Toshio in their thieving gang, with Hitomi (who is also Toshio's girlfriend) materially attempting the job with her hair dyed blonde and green contact lenses. At first she's just doing the attempts and flirting with him... But at one point Hitomi realizes that she's jealous of the blonde Cat's Eye, and the blonde Cat's Eye is jealous of Hitomi!Hitomi openly wonders what's wrong with herself...
Batman is Batman, Bruce Wayne is mostly a construct. Maybe.
In Batman Beyond he realizes that his voice telling him to kill himself was a fake when it referred to him as Bruce. "That's not what I call myself in my head."
Then Terry asks him, "What do you call yourself?" He gets a look.
Terry: Remember, that's my name now.
Bruce: Tell that to my subconscious.
One Batman Expanded Universe novel implies that Bruce Wayne has, in fact, "subdivided" his mind between the two separate identities, and that the "Bruce" aspect is physically weaker than "Batman", despite Wayne's training.
The extent to which this is true varies over time, tending to oscillate from one extreme to the other in a manner reminiscent of a Cyclic Trope. As of October 2007, most current portrayals are tending away from this trope; no doubt it will change back in a few years. And given the speech about Bruce being the mask at the end of Batman Begins, and the way movies tend to set the next few years of the comics they're based on, that may already be starting.
In the "Batman RIP" storyline a villain-induced psychological trauma "kills" Bruce Wayne, and as a result, Batman takes on an emergency backup persona as a garishly-costumed version of "Batman without Bruce" and goes around Gotham beating criminals with a Bat-bat along with a (maybe) hallucinatory Bat-Mite. Which was a Crowning Moment of Awesome for being a homage to a classic Silver-age story about Batman encountering another Batman in a distant galaxy. One of trademarks of Grant Morrison's run is the reincorporation of so many bizarre silver-age stories.
The idea was deconstructed during the "Bruce Wayne: Murderer/Fugitive" storyline. In an issue leading up to the arc, Bruce was toying with the idea that while Batman can't kill, his alter ego Matches Malone can (he backed down from that). After being framed for murder, going to prison and then escaping, Batman decided to abandon the Bruce Wayne identity entirely, losing most of his compassion in the process. The rest of the Batfamily are shocked when he tells them point blank that there is no Bruce Wayne, and refuses to answer Nightwing when he asks who adopted Dick Grayson if that's true. One of the main writers for the storyline summed it up pretty well. "Somewhere in the Bat Bible, it's written 'Bruce Wayne is the mask, not Batman. Oh, and he's not crazy'. That always bugged me. If that's not crazy, then what is?".
In Arkham Asylum, when he's captured by the Joker and the inmates want to take off his mask, the Joker tells them not to be stupid; that mask is his face.
Recently, Grant Morrison has been trying to establish in his recent Batman works that there is no "Bruce is Batman's mask" or "Batman is Bruce's mask" since it was that kind of thinking that nearly destroyed him just around the time that Infinite Crisis was going on. So Bruce Wayne attempted to rid himself of his demons and start anew during the missing year. Nowadays, he is both Bruce Wayne and Batman, neither less than the other, both more human than either one could be alone. One blogger (Chris Sims) cleverly pointed out that not only does Batman fight crime, but Bruce does as well through humanitarian efforts such as funding rehab centers and hiring former criminals at Wayne Tech to help them get a fresh start. Furthermore, he remembers each of them.
Bruce's humanitarian work really took off during No Man's Land, where he actually took time off as Batman to fight congress, among other things, as Bruce Wayne. Also, this is where Dick Grayson decides to become a cop (thus fighting crime as both Dick and Nightwing) and Batman tells him "You're better than me, Dick.", saying he has made both Robin and Nightwing "an extension of who [he is]", rather than just becoming the mask.
This is also the path that The Dark Knight Saga took from the start. The playboy idiot Bruce Wayne "persona", such as it is, was a kind of on the spot bullshit maneuver Bruce used to deflect suspicion. Judging from his immediately previous living conditions, Bruce never has been that sort of man.
The Batman Inc arc seems to be suggesting that the Batman mask isn't exclusive to Bruce Wayne.
Many would say that the truest Bruce is the detective in the cave, in costume but not the cowl, often with his True Companions at his side.
A parody/homage of Batman, Darkwing Duck, created the identity of Drake Mallard on the fly in order to give his newly adopted daughter a somewhat normal life. There's no conflict, though, as he doesn't really act any differently, and finds being "civilian" very insipid. Fortunately his neighbors are not very bright.
Later episodes revealed that Drake Mallard actually was his civilian identity, before he became Darkwing, but the beginning episode "Darkly Dawns the Duck" makes clear that he had not been using his civilian identity for quite some time, living full-time as a superhero. (Questions of how he does the grocery shopping, and where he gets his income, and other such mundane trivia are conspicuously never answered, and this is even at one point lampshaded.) The episode "Clash Reunion", in which the superheroic identity was invented, made it very clear that Drake Mallard was exceedingly unpopular, while Darkwing Duck was an instant success. The intensely egotistical and vain protagonist probably began neglecting his civilian identity as soon as possible for this reason, until Gosalyn gave him a compelling reason to take it back up.
The comic revival does answer a few of these. DW receives a stipend from S.H.U.S.H., presumably under the guise of a tester, (with all the gadgets and whatnot). When he temporarily retires, he is forced to take up a menial office job, (and isn't happy about it one bit) Launchpad probably does most of the shopping, laundry etc. which eventually backfires in a BIG way.
Dick Grayson publicly fought "Nightwing" in order to legally marry his long time girlfriend Koriand'r/Starfire, as Nightwing doesn't exist on paper. Too bad the wedding was crashed by an ex-teammate turned evil...
It was really more about his previous habit of dating her in various disguises. She was getting a bad reputation for "cheating" on Nightwing. Of course given how bad the Titans of that era were at keeping Dick's identity secret, one wonders why the bothered.
Spider-Man is mostly Peter Parker. The witty quips he makes when fighting supervillains are usually belied by his internal monologue about his life as Peter Parker. On occasion, though, after a particularly traumatic adventure, he has sealed himself up behind the Spider-Man persona, and once or twice, a darker persona, referred to as "The Spider", has emerged.
Peter David did a series where Peter Parker was locked up and doped up in a sanitarium, where Peter came to terms with "The Spider". And it wasn't particularly darker than Peter or Spider-Man.
"The Spider" is the nickname his Rogues Gallery has given to Spider-Man whenever he's not talking and joking. This more than anything else scares the crap out of them.
A few instances have suggested that Spider-Man is essentially the GIFT version of Peter Parker. Peter Parker is normally introverted and socially reserved. Spider-Man is Peter Parker with anonymity and an audience and as a result his own social restraint has been removed. Spider-Man is much more assertive and has an inability to stop telling bad jokes.
The Green Goblin is a rare villainous example, one of the few bad guys who continues the life of a secret costumed villain long after being exposed (to the hero and readers, and then even to the in-universe public). In his case the identity problem is due to actual mental illness, as he suffers from schizophrenia, manic depression and psychotic breaks from reality, and originally and occasionally full blown multiple personality disorder, not to mention the odd bout of Identity Amnesia, and this all apart from his base anti-social, obsessive-compulsive, paranoid and narcissistic tendencies. To explain:
Norman Osborn originally was basically a bad man, a Corrupt Corporate Executive at the best of times, struggling with being a single father and his own anger problems, while engaging in barely legal activities aimed at increasing his money and power.
The Green Goblin is his Ax-Crazy alter ego he originally assumed after the accident that gave him superpowers caused him to snap, and became a sort of fantasy life for him to live out his more megalomaniacal dreams in, such as controlling the criminal underworld. The Goblin is violent, sadistic, reckless and utterly psychopathic, and represents Osborn's homicidal impulses. Osborn is initially not in total control of himself as the Goblin and, if pressed (such as reminding Osborn of his son) the Goblin can manifest as a Split Personality who will argue with the slightly meeker Norman.
Osborn became nicer after his first bout of amnesia; his first thoughts were to ask where his son was. He seemed shaken by his previous events even if he didn't quite remember what happened, but though he seemingly made a genuine effort to be better around people - notably supporting Peter - he could still engage in petty and morally questionable acts; in a retcon it was this Osborn (subconsciously with the Goblin) who took advantage of Gwen Stacy, and suffered from anger and stress problems that, when they overwhelmed him, resulted in the goblin taking over.
Finally, following his record breaking 27-year Comic Book Death, Osborn came back and this, the modern version, is generally considered to be the "real" Osborn, the man he always wanted to be - a confident, disciplined, wealthy, ruthless, sadistic power-hungry sociopath with a positive public image who swings from seeking bloody vengeance on Peter Parker, to viewing him as a surrogate son and trying to turn him to the Dark Side, to simply resigning himself to enjoying their "games" and viewing their fights as a fun hobby that saved him from a life as "just another boring industrialist". For a long time, he appears to have his mental issues more or less under control and the Green Goblin becomes basically just a costume he puts on for thrills or when he needs to get his hands dirty. However, during Dark Reign, the Goblin persona starts assuming a life of its own again and he finds it harder and harder to control his murderous and maniacal urges, eventually killing subordinates for petty criticisms and even painting his face green during the final battle.
Superman goes up and down the spectrum, depending on series and writer. During the Silver Age, the "real" persona seemed to be Kal-El; Post Crisis, it's more Clark Kent. He's always "Clark" with his adopted parents, though. A key point in the plot of Kingdom Come is that Superman has begun to lose his humanity, becoming less "Clark" and more "Kal-El".
One Bronze Age (i.e. after the Silver Age, but before the Crisis) story featured Superman getting infected by a Kryptonian disease. The disease causes hallucinations comprised of two figures, similar to a Good Angel, Bad Angel, one of whom thought he should accept it because death comes to us all, while the other one insisted he had a duty to fight it off. The defeatist appeared as an empty suit with glasses hovering above it, and the fighter as an empty Superman costume. Both referred to him as "Kal" and to each other as "Clark" and "Superman". At the end he wakes up, insisting he invented both of them, and neither are real.
In team-ups with Batman, it is generally accepted that Superman is the mask of Clark Kent whereas Bruce Wayne is the mask of Batman. The idea is that (implied or not, even true or not in the universe at the time) these relations reflect the divergent nature of the two. Bruce is a human that has grown to hate humanity and has symbolically abandoned it, embracing darkness. Clark Kent on the other hand is an alien that has largely embraced the ideas of humanity (in some continuities, he has gone so far as to embrace them for a lack of morality in his Kryptonian heritage e.g. in Smallville, many Kryptonians believe him to be weak for caring for the Puny Humans), and finds strength in the light.
This aspect is probably best demonstrated in Lois and Clark when - during a phone conversation with his parents, they warn him that he's started talking about himself in third person.
Notably: In the scene he refers to both Clark and Superman in third person.
But in another scene in Lois and Clark, after Lois finally understands the real relationship between Clark Kent and Superman, he says "Superman is what I can do. Clark is who I am", which contradicts the points above.
The revised Superman: Birthright posits that Clark Kent and Superman are masks, and that the "real" Kal-El is "Smallville Clark", i.e. the way he acts when around his parents and close friends who know his true origins.
Essentially, Clark Kent, renown reporter, is the man he must be in order to protect the secrets of Superman, who is the man he must be in order to fulfill the moral obligations he feels.
Smallville provides a new option. Superman is the real persona, but only because that's the man Jonathan and Martha Kent raised him to be.
Or perhaps more precisely: Superman is Clark Kent, minus the need to keep his abilities secret.
Superman: The Animated Series makes it pretty clear that Clark is the real identity. In "The Late Mr. Kent", when Clark Kent "dies", Superman is much more upset about it than Ma and Pa Kent.
Pa Kent: It's not like he's really dead Martha, he just can't be Clark anymore.
Superman: But I AM Clark, I NEED to be Clark, I'd go crazy if I had to be Superman all the time!
"Superman was born Superman. When Superman wakes up in the morning, he's Superman. His alter ego is Clark Kent. His outfit with the big red "S", that's the blanket he was wrapped in as a baby when the Kents found him. Those are his clothes. What Kent wears - the glasses, the business suit - that's the costume. That's the costume Superman wears to blend in with us. Clark Kent is how Superman views us. And what are the characteristics of Clark Kent. He's weak... he's unsure of himself... he's a coward. Clark Kent is Superman's critique on the whole human race."
"Remember, Kent was not Superman's true identity as Bruce Wayne was Batman's or (on radio) Lamont Cranston, The Shadow's. Just the opposite. Clark Kent was the fiction... Superman only had to wake up in the morning to be Superman. In his case, Clark Kent was the put on... The truth may be that Kent existed not for the purposes of the story but the reader. He is Superman's opinion of the rest of us, a pointed caricature of what we, the noncriminal element, were really like. His fake identity was our real one. That's why we loved him so."
Even during periods where "Clark Kent" is just a persona, this is silly. Those things are disguise tactics—he's cowardly, etc. because Superman isn't, so obviously he isn't Superman.
Others accept the premise that Clark is the mask, but come to the opposite conclusion. That Clark Kent is what Superman thinks a man ought to be. Thus Clark is the "good side", and evidence of Superman's admiration for the human race, which can produce men of good character despite the lack of physical power that he has. This concept was best demonstrated in the famous Superman vs Clark Kent scene in Superman III, (usually agreed to be the only redeeming scene of that movie).
It's even brought to a head in Superman: Man Of Steel #96, when Kem-L (manifested by the Kryptonian Eradicator program) comes to "cleanse" Superman of human infestation, calling him "Kal-El" and telling him to fulfill his legacy. The response?
In a story arc from Superman #296-299, Superman finds himself with a "split-effect", leaving him with no superpowers while wearing civilian attire. He decides to spend at least a week as Clark and finds that he has more backbone — standing up to those who antagonize him as Clark, being more romantic with Lois, and engaging in a low-gravity battle with Intergang. However, helplessly watching huge disasters unfolding was too much for him to bear. Later, he decides not to fall back on Clark as Superman, forced to be fully committed to world welfare and leaving him unable to unwind and spend time with his muggle friends. In the end, he decides not to discard either identity, and figures out the source of the split-effect in time to stop the years-long scheme of The Chessmaster trying to destroy the world.
There's a very, very fun story in JLA #51-54 where Superman's wish that the League's members didn't have "two lives" is granted by a sixth-dimensional wishing machine. Hilarity spectacularly fails to ensue, and only Wonder Woman and Aquaman are exempt due to having no dual indentities at the time. In the end, the aliens who gain control of the machine split them too. Aquaman finds himself in human and amphibian forms, while Wonder Woman is separated from clay, and she saves the day as the spirit of truth.
Clark Kent without Superman becomes truly timid and afraid of heights, while Superman without Clark loses touch with humanity ("call me Kal", changing to a Kryptonian-style costume).
Bruce Wayne without Batman has no outlet for his rage at the corruption of the world (beating two thugs nearly to death over spray-painting his car), while Batman without Bruce has no motivation and barely speaks - beneath the mask, he has no face.
"Everyone figured if you split Batman and Bruce Wayne, you get a fop and a lunatic - what we didn't guess was which would be which."
Kyle Rayner without the ring goes near-crazy without it to use for self-expression, covering his apartment with drawings that can't compare to what the ring would create, while Green Lantern becomes a war machine without humanity and creativity.
Wally West without The Flash becomes lazy and apathetic, while the Flash forgets the legacy of those who came before him.
John Jones freaks out when he becomes telepathically "blind", but is fascinated by his invulnerability to fire and the loss of his Last of His Kind origins.
Eel O'Brian returns to his thieving past while Plastic Man loses track of everything but his clowning.
Eventually, it's Eel who realizes that everyone is slowly going nuts while separated and assembles the civilian identities to join back up and save the world as just six dudes. The message? The man behind the mask is both, or it doesn't work - for example, Superman is at his truest when he's at home in Smallville being Clark Kent with superpowers.
Christopher Chance, The Human Target, is a private detective/bodyguard who protects his clients by impersonating them to draw any would-be killers out. However, in modern stories, he is so good at his impersonations that he sometimes forgets his own identity in the process.
Rorschach in Watchmen takes it so far that he calls his Rorschach-test-shaped mask his "face"; when he's unmasked, he screams at the police for them to give his face back. He claims that before he had to Shoot the Dog he was simply "[Walter] Kovacs pretending to be Rorschach" and now it's the other way around.
Another indication of this is in one flashback to before Rorschach's Becoming the Mask moment, where we see him speaking normally instead of with his usual wobbly speech bubble and font. It's no wonder the prison psychologist slowly starts to think of him as Rorschach instead of Kovacs.
Unlike Superman, Wonder Woman was not raised by mortals, which makes all the difference. For some time in the Silver Age, she was a full-time civilian. For about two decades Post Crisis, she had no secret identity at all. At all times, the Amazon Princess Diana is basically the real her.
A Secret Wars spinoff had the Thing fight his Ben Grimm persona to the death.
One of the more unique aspects of the X-Men is that they seem to have variable degrees of separation between their "superhero" and "civilian" personae. This is intentional: being a mutant isn't exactly something they can stop doing if they want to retire, and is often explicitly used as a metaphor for real-world ethnic, sexual, and religious identities. For example, many of the X-Men don't wear masks of any sort (Shadowcat, Emma Frost, Professor X, Beast) and seem to live quite openly and proudly as mutants. Others will go to some extremes to hide who they are and will adapt quite elaborate secret identities (Nightcrawler, Angel) including the use of holographic projectors to make them appear "normal." This is even reflected in their codenames, which over time have become more like nicknames than any kind of serious attempt to hide their real names. Some have just dropped them all together, while others have started using them all the time, even in private conversations or when not in costume.
Archangel (Warren Worthington) cited Native tradition that the mask was an expression of true identity when confronted by X-Factor (former X-Men) members with an "I Know You're in There Somewhere" Fight.
IIRC, in Ultimate Marvel it was originally explained that their original names were (if you will) "slave names", and their codenames were effectively their new "real" names. (This reflected the continued influence of Magneto's ideology on Professor X even after their breakup.)
Booster Gold is an interesting example, as his secret identity and his real identity are still Booster Gold. To the whole world, especially the superhero community, he presents himself as a selfish, bumbling fool who will do anything for fame. Secretly, he's a true and noble hero charged with protecting the timeline.
Even before Booster took up his role as timeline defender, he lacked an alter-ego - he was Booster pretty much all the time. Of course, his civilian identity hasn't been born yet.
Steve Rogers is really Captain America, so much so that it's hard for him to be a normal person. There was an incident in one Captain America comic where Cap confided to Hawkeye about how uneasy the hero worship made him feel, how he was worried about being mobbed whenever he went out, etc. Hawkeye responded by pulling Cap's mask off and saying something along the lines of "Yeah, I can see how that would be a real problem, Steve!" - Cap had to be reminded that he didn't have to be Captain America all the time, that he could take the mask off and just be an ordinary person.
In effect, his costume is mostly just for protection and identification during fights rather than any sort of means to conceal his identity. Thus he doesn't see it as a mask but just something he wears.
This happens with Thor and his various alter egos A LOT, primarily because most of those alter egos are actual, separate entities; Donald Blake was a construct created by Odin for Thor to inhabit to learn humility, and Eric Masterson and Jake Olson were human beings whom Thor bonded with to save their lives. The only "classic" secret identity Thor maintained was construction worker "Sigurd Jarlson", essentially Thor in street clothes and Clark Kent-ish glasses with his hair tied back.
Moon Knight, a Marvel Alternate Company Equivalent to Batman created a bunch of different personas to facilitate his crime fighting, but is often depicted as mentally disturbed and unsure of his true identity.
The Batman-is-real-Bruce-Wayne-is-the-mask idea is invoked but averted for Kate Kane in Batwoman #0. Her narration says the obvious idea would be that Kate Kane went on Training from Hell, and Batwoman returned. In fact, the confused woman who left didn't know who she was, and it was only once she became Batwoman that she felt like Kate Kane again.
Similar to the Heinlein novel below, the film Dave features a U.S. President that's had a stroke, putting him in a coma some corrupt politicians don't want anybody to know about, prompting them to hire a guy already working as a look-alike for the President to step in and replace him. His sudden exposure to the weight of the burden on the President inspires him to turn on said crooks and try to improve the country.
The Revealreveals that the former president was even more corrupt than the bad guys, and Dave was a better president than the real one ever was.
Star Wars: Boba Fett's identity as a bounty hunter is often considered his True Self, while the identity he uses without the armor is often considered a facade. At one point, after escaping the Sarlacc on Tatooine, he was tended to by rival hunter Dengar and an amnesiac palace servant of Jabba the Hutt's. Seeing him without the mask, she quipped, "THAT'S his face?" to which Dengar responded, "No, that (the mask) is."
In the first live-action Spider-Man movie, there was an absolutely fantastic scene where the demonic Green Goblin and his human identity (the guy who wore the suit) talked to one another. There was only one man in the room...
In The Long Kiss Goodnight Geena Davis' character is an amnesiac schoolteacher. Turns out she was really an assassin with a head injury who ended up believing her cover. As she is much happier as a schoolteacher than an assassin it could be seen as a subconscious choice to live the mask.
In the film version of Harry Potter and the Goblet of Fire, Lucius Malfoy protests his loyalty to Voldemort, saying that the face he presents to the masses is the real mask, and that his Death Eater mask is his true face.
The silver-age Superman is referenced by Bill in Kill Bill (Volume 2): Superman has to put on a show of being Clark Kent, but beneath the surface he's Superman all the time.
Some reference material for Indiana Jones raises the question of whether his "real" self is the mild-mannered (yet charismatic) professor Dr. Henry Jones, or the globetrotting adventurer Indiana Jones. Although neither identity is really a secret from the world or ostensibly separate from the other (he still conducts "archaeology" as Dr. Jones either way), it's implied that even he isn't sure.
V from V for Vendetta may apply, with the rare case that we never learn his original identity. Still he is very clear that the V mask is his true face:
V: There is a face beneath this mask, but it's not me. I am no more that face then I am the muscles beneath it, or the bones beneath that.
The question is begged of Bruce Banner in a deleted scene from Avengers: "Are you a big guy that gets all little, or a little guy who sometimes blows up big?" Banner himself is unsure of the answer.
In Robert Heinlein'sDouble Star, an actor on the rocks is hired by a kidnapped politician's (whom said actor does not particularly agree with) aides to impersonate him until he can be rescued, more and more becoming the politician as time goes on. Just after the politician is rescued, he dies from the after effects of his kidnapping, prompting a Downer Ending where the actor must sacrifice his own life to uphold the ideals he has now come to support.
Wraith Squadron'sLara Notsil again. In this case, rather than being a result of past trauma or a secret superhero identity, her problem stems from a very real conflict between who she wants to be be, and who her Imperial intelligence instructors have trained her to be. The rigorous, cruel methods used by her teachers, the constant assertions to assume her roles flawlessly because nothing else was of consequence, and the dictum to abandon everything, including emotional attachments, that would interfere with her fulfilling her mission is enough to mentally unbalance her for a time. Not only does there come a point when she is (briefly) no longer certain who she is, Lara or Gara Petothel, but she even finds herself missing Kirney Slane, a practice identity from her early days at the Academy, because Kirney's life was so much simpler and more carefree. This same identity is later adopted by her when her identity is exposed and she must take refuge with Zsinj, because she views Lara as having "died".
In the Dexter novels, Dexter refers to the drive inside him to kill as his Dark Passenger. In the third book, the Dark Passenger is revealed to be a demon possessing Dexter. When it temporarily leaves his body, he is unable to kill.
Until things came forcibly to a head in Lois McMaster Bujold's Memory, Admiral Miles Naismith of the Dendarii Free Mercenary Fleet had respect, love, and quite a bit of power. Unfortunately he was also Lt. Miles (Lord) Vorkosigan, Barrayaran Imperial Security; bound by duty, oaths, and blood to a backwards world where many still regarded him as a twisted little freak that should have been euthanized at birth. It did not help that he had fallen hard for one of the few people that knew the whole story and who, for all that she loved him back, still saw life as Lady Vorkosigan to be something akin to a death sentence.
Miles Vorkosigan: Dammit, sir, what would you have of me? The Dendarii are as much Barrayaran troops as any who wear the Emperor's uniform, even if they don't know it. They are my assigned charge. I cannot neglect their urgent needs even to play the part of Lieutenant Vorkosigan.
Captain Galeni:Play the part of Lieutenant Vorkosigan? Who the hell do you think you are?
Not to mention Miles' mother's comment that the personality of "the little Admiral" is key to keeping Miles, not sane (she explicitly doesn't believe he is sane) but FUNCTIONING.
The clowns of the Fools' Guild in the Discworld novels tend to regard their painted faces and squeaky noses as their "real" faces. Discovering this becomes an important plot point in one of the City Watch novels.
In Maskerade, the character who's secretly the OperaGhost gains an immense amount of confidence and sheer grace from wearing the mask and not appearing as himself. In the end, the witches convince him he now has a permanent, invisible mask, and he becomes an entirely different person permanently. Too bad "Becoming the Mask" means something else, because it would fit here perfectly.
Though none of them wear actual masks, several of the Seekers of Truth are this way, especially the Wizard. Especially telling is when the Seekers are disbanded, and half of them stay on with the city to train the new SWAT cops.
The John le Carré novel A Perfect Spy is about a character (somewhat of an Author Avatar) who gets early training from a con artist father and for a time applies those skills as a agent, but eventually falls apart because of all of the different personalities he had maintained
The Bradley Denton short story We Love Lydia Love featured a man who is bribed to form a relationship and then break up with a singer-songwriter, in the hope of getting her to write a new album fuelled by the breakup (that's how she rolls). He has a chip in his head, containing the consciousness of her dead lover, intended to make it easier for him to fake being her perfect man. After a while, he begins to identify as much with the dead lover as with himself, and decides to stay that way and spend his life with the singer. The story goes all sorts of places you wouldn't expect.
Cantra, of the Liaden Universe books, was raised as part of a society of assassins who used Secret Identity Identities to infiltrate their targets. In Crystal Dragon, she becomes so subsumed in her role as a scholar that she cannot treat her companion as human and furthermore nearly dies in a knife fight (dissertation defense is Serious Business for these scholars) because she's locked away all of her reflexes.
Edmond Dantes in The Count of Monte Cristo was so changed by prison that as the Count, he doesn't look at all like the idealistic Nice Guy he used to be and has some That Man Is Dead toward his earlier self. Also odd is that Dantes creates other personas: Busoni, an intellectual and pious Italian priest who seems to be modeled after Faria who tutored him in prison, and Lord Wilmore, an eccentric British philanthropist who is an enemy of the Count. Thus, Dantes essentially divided the different parts of his personality into different identities, and his main identity as the Count represents his darker side. He ultimately ends up showing some kindness and mercy (after one of his revenges went too far), and at the end of the novel signs a friendly letter as "Edmond Dantes, Count of Monte Cristo", thus reconciling the identities.
Silk, the artful thief from The Belgariad and The Mallorean, has cultivated a wide range of alternate identities, each with its own name, personality and unique quirks. At one point he says that he probably lost track of his True Self years ago. Even his birthname and identity has become a facade.
This is apparently true of his entire country, or at least the Diplomatic Corps (and it's not safe to assume those peasant farmers you just passed on the road blind stinking drunk and smelling of pig dung are not actually in fact in the diplomatic corps, stone cold sober, and bearing the title "Duke" in some other identity).
The Shadow's real name was Kent Allard in the pulp stories, where "Lamont Cranston" was one of many disguises (as well as an Identical Stranger who grants Allard the use of his identity). The radio series simply shaved off one instance of "Identity".
Live Action TV
Chuck revealed a very similar backstory for Sarah, as was the case in The Perfect Spy: her father was a con man who ended up in prison after scamming some dangerous people. Even as an outcast high school student she had become involved in these cons and used a number of fake identities, but following the father's arrest, she was approached by the CIA whose extensive training resulted in the very different character in the show.
El Chapulín Colorado has no secret nor civil identity, and in one episode is ouright stated that Chapulín Colorado is his real and legal name. Word of God also says that he ditched any semblance of civil identity long time ago; he is El Chapulín Colorado full time. Because this is a Half Hour ComedyAffectionate Parody of superheroes, the implications are never explored.
An episode of Criminal Minds featured an con artist who began killing his marks because he started suffering breakdowns between his fake personas and his real identity at inopportune moments, causing him to make mistakes that the victims noticed.
Played with on Cheers when Norm starts a small housepainting business and hires three guys to be his workers. The workers end up being lazy slackers and Norm is too nice to yell at them or fire them. He creates an imaginary persona for himself, "Anton Kreitzer" a mean, dictatorial Bad Boss who only communicates through phone or through Norm to to get his his workers to stop slacking off. He goes so far as to rent an empty office and hiring a secretary for Kreitzer. When the workers get angry and try to confront Kreitzer about his harsh treatment they find the empty office. They come to the conclusion that Norm the nice guy was fake and that Kreitzer is the real identity!
The first Metal Gear Solid has Decoy Octopus, an operative of FOXHOUND capable of imitating other people perfectly, even going to the length of draining their blood and putting it in his own body. He has to go through psychological conditioning after every mission, due to the extent he "becomes" the other person.
In Metal Gear Solid, a repeated theme is Solid Snake's namelessness - villains accuse him of 'not having a name', and Snake implies as such when Meryl asks him for his real one. His desire to live a normal life is symbolised by him introducing himself as 'David' to Meryl/Otacondepending on the ending you get. In the original draft of Metal Gear Solid 2, Otacon was to call Snake 'Dave' when the two of them were in private, but that was dropped for good, leading to the impression that Snake thinks of himself as 'Solid Snake' and not as David. According to the MGS Database, though, he has the people around him start to call him David after the events of Metal Gear Solid 4.
This was meant to be an in-joke reference to 2001: A Space Odyssey. If you get the Otacon ending, he replies "HAL and Dave, that's a good one."
And possibly the fact that David is the name of Snake's voice actor.
Both Evil Spinnerette and Mecha Maid from Spinnerette refer to their normal names as their "given" names, though Spinnerette still considers her superhero self the fake identity, though that is starting to unravel, as she can no longer comprehend life as a normal human To the point she'd rather die then be human again.
Jem often realized that she was "jealous of herself" and had to be manipulated by her own supercomputer into maintaining her Secret Identity.
Batman Beyond: As mentioned in the Comic Books section, it's shown at the end of season one's "Shriek" that Bruce has it all figured out.
Bruce Wayne: The voice kept calling me Bruce. In my mind, that's not what I call myself.
In Transformers, Punch is an Autobot who masquerades as a Decepticon named Counterpunch to gain information. In the Dreamave continuity, he starts suffering blackouts as Counterpunch; it is likely that if Dreamwave had not gone bankrupt, Punch's character arc would have involved such a situation.
Darkwing Duck has the titular character the real persona while Drake Mallard is a made-up.
It's a little more complicated than that. Later episodes reveal that he WAS Drake Mallard before becoming Darkwing, but until he adopted Gosalyn he had been neglecting his civilian identity. Considering that the main character is rather egotistical, it was probably in no small part due to the fact that Darkwing Duck was much more popular than Drake Mallard.
Young Justice: Miss Martian wants to be known by her shape-shifted "Megan" persona, and definitely not as a white Martian.
Truth in Television. Some musicians and artists are known to have issues about losing their identities in some fictional construct, such as David Bowie, Alice Cooper, Eminem, and Shiina Ringo. This is one of the plot points in Man On The Moon, a biopic of Andy Kaufman. Another infamous example is Peter Sellers who stated "There was a me, but I had it surgically removed" on the Muppet Show. See Alter Ego Acting.
In fact, Sellers' fascination with Chance the Gardener stemmed from this. Preferring to lose himself in characters to set aside his own personal flaws and make audiences, those close to him, and himself happy, Sellers was quite understanding of Chance's situation as someone who made others happy solely by reflecting what others wanted.
According to some who have worked with him, satirist Daniel Whitney is slowly vanishing behind Larry The Cable Guy (which has also gone from being a satirical character he did at the end of his stand up routines to being the whole thing and losing the satire). Talk about Nightmare Fuel...
It's very telling that even in an interview with 60 Minutes, Whitney appeared in character as Larry—somewhat muted from his on-stage behavior, but still very much Larry. Either Whitney is dedicated to the pretense that Larry the Cable Guy is who he really is, or the Whitney of his initial stand-up career was the real pretense, and he's a better actor than anyone gives him credit for.
One concerning thing is that when he voiced Mater for Cars, he requested to be (and was) credited as Larry the Cable Guy, not Daniel Whitney.
David Bowie has stated in interviews that he's terrified of the possibility of completely becoming Ziggy Stardust. He stopped adopting such specific stage personas in 1977, after — with the "help" of his cocaine addiction at the time — the heartless Thin White Duke of Station to Station came close to consuming him.
Hell, it's not just famous people — "Witty Ticcy Ray", a Tourettes sufferer (including a limited degree of Tourettes Shitcock Syndrome) in The Man Who Mistook His Wife For A Hat believed he had to fight off his disorder from eclipsing his real personality.
Former professional wrestler The Ultimate Warrior changed his name from Jim Hellwig to Warrior after leaving wrestling. Almost all the wrestlers who worked with him recounted him as being an egotistical asshole even outside the ring. But all those wrestlers mostly worked with him after he'd gotten famous. The people who'd known him before recounted that Jim Hellwig was a nice, soft-spoken friendly guy. Jim Ross suggested that he'd ended up fighting his in-ring persona, and the persona won. As he got more famous, the moments where he was Jim grew less and less.
In Beyond the MatVince McMahon says of Jake the Snake: "I was never able to tell the difference between Jake Roberts the performer and Jake Roberts the person, because frankly I never knew which one I was talking to. I don't know that they're not the same."
El Santo lived in his wrestling mask his entire career, going so far as to have chinless masks that allowed him to eat while costumed. He briefly removed the mask just once in an interview to bid goodbye to his fans. He was even buried in it.