Asteroid Runner hosts a couple of these, mostly because every member of the eponymous ship's crew seems to be trying to hide things.
Noa: cultural fish-out-of-water who makes due with what she has, or egotistical alien who forces her culture on everyone by refusing to dress and act like the rest of the crew.
Theory has some weight, given seemingly 90% of the times Noa gets in trouble, it's cultural dissonance issues.
Gerard: keeping secrets from Izzy really for her sake, or just selfishly witholding information, afraid of losing his best friend and love interest?
Locke: Is his obsession with being called a 'marksman' really all about being outclassed by the Sniper in Green or is he traumatized by the cold killing of his squad and wants to call himself anything but a sniper to avoid connecting himself with the murders he's committed.
It doesn't help that he calls himself a marksman. A marksman could be a shooter of targets just as much as a shooter of people. Sniper directly implies shooting people.
The whole point of A Very Potter Musical. And it works through Character Development or the new characterizations being a hundred times funnier then canon. In fact Hermione is about the only person close to canon. Just some examples:
Harry and Ron are now huge jerks and Harry has a huge ego. But they learn.
Draco is a petite Small Name, Big EgoCloud Cuckoo Lander whom no one can stand who is obsessed with a space school called Pigfarts. He also joins the heroes through a Heel-Face Turn, is in love with Hermione only to hook up with Luna Lovegood and is the biological son of Dobby.
The short story ''Chaos Theory'' is built on this trope as every almost every character named in the course of the story can be seen as the worst/ultimate villain. Oddly while the site it is hosted in is clearly not safe for work the story contains essentially no explicit material.
And for that matter, is Captain Hammer really a malicious, spiteful guy who wants to hurt everyone, or just an idiot whose morals have been warped by having ridonkulous superpowers?
Did he date Penny purely to spite Billy - wanting his nemesis's attention (and other things) for himself? Guess there's always the possibility that he actually liked her, but...
It's more than a possibility, since Penny and Captain Hammer had Love at First Sight and spent all weekend together before Hammer knew Billy had a crush on her. And he's actually considering sleeping with her a second time - something he's never done with a girl before!
Maybe he was hopeful about sleeping with her twice, something he was excited about because most women realize how much of a jerkwad/dork he is quickly enough to keep them from going back for seconds. This is supported by his apparent pride in the concept of even having slept with her in the "Everyone's A Hero In Their Own Way" song.
After Penny's death, does Billy embrace his dark side completely and join the Evil League of Evil, or briefly consider it and instead go back to just being a normal guy out of regret, making the ending montage a fantasy like the Brand New Day montage?
Amnesty of the Global Guardians PBEM Universe. On the one hand, she's an amazingly powerful superhuman who uses her abilities to aid people who are starving, who are sick, who are war ravaged, and who are drought-stricken around the world. On the other hand, she's listed as a terrorist by the governments of thirteen different countries for some of the things she's done to aid these unfortunates (slaughtering the army of one particular South American dictator because they were "pacifying" a rebellious peasant village is the best example).
Unlike most Machinima which create their own original characters, the characters of Melee's End are just Alternate Character Interpretations of the game's characters.
In the Netflix original series Orange Is The New Black, just how gay is Chapman? Is she bisexual, as she initially appears, or is she completely gay and just in denial about it? She seems much more passionate about Vause than she ever was or could have ever been about Larry. When the other inmates in "Bora Bora Bora" make her out to be some kind of lesbian rapist to scare Dina and the other girls as part of the scared straight program, the part she objects to is that she's completely gay. She then tells Dina, the girl in the wheelchair, that the scariest part of being in prison is having to confront your true self. What about her true self frightens her so much? Maybe the fact that she's not bi, she didn't go through a phase in college, she's not going through Situational Sexuality in prison; she's just completely gay.
Is the Director of Project Freelancer in Red vs. Blue a Well-Intentioned Extremist who Did What He Had To Do or just plain evil? He clearly considers himself the first, arguing that his manipulation of the Freelancers, torture of AIs, and lying to/stealing from the UNSC was all for the sake of winning the war (against aliens? against Insurrectionists? He's vague). On the other hand, he induces multiple personality disorder in an AI (multipleAIs, potentially), is responsible for Parental Neglect, and seems to put getting his dead wife/girlfriend back above the life of his agents, up to and including his daughter.
An interesting fan theory regarding Doc makes use of an Alternate Character Interpretation. Most people view Doc as a cowardly and inept medic. However, he knows a surprising amount about Project Freelancer even before anyone else finds out, such as potentially knowing the Red and Blue bases are only simulation bases. Because of this, an alternate interpretation is that he was a Freelancer agent sent to keep an eye on Alpha (and Beta?) who fakes his poor medical skills to throw suspicion off of him... and to be able to get rid of anyone Command doesn't want around anymore.
Retsupurae's takes on MuscleBomber2021 (who is desperately trying to impress a girl named Amy with his Super BummermanBomberman 2LP) and Billy MC (whose parents force him to play Mario games and give him McDonald's food as christmas presents).
The last post of Seeking Truth offers one of these for its protagonist, Zeke. Until then, he was something of a Memetic Badass due to defying Sanity Slippage as best he could, actually scrabbling for a way to take the fight to the Slender Man, and leaving a Do Not Go Gentle speech before doing so. Then, in Status Report, we learn that the traps he set up in his home killed at least one stranger, and he seemingly hid the body in his garage for weeks.
Similar to the above, the ending of Dreams in Darkness leaves us wondering if the protagonist, Damien just a paranoid schizophrenic who snapped after the bloody murders of his closest friends and attributed it to Slender Man (who might or might not actually be responsible for one or more of those murders), hallucinating Mr. Thin everywhere and losing track of where "reality" ended and "Alternate Reality Game" began.
Smallvillains likes to provide these for its characters, derived by deliberately watching Smallville episodes without research or context. Thus far Clark is a Pinball Protagonist, Lana is flat-out crazy, Lois is actually the Silver Age Jimmy Olsen, and the Kents are assholes who drove Lex Luthor to villainy.
A common comedic tool for TheStrawhatNO! and happens at least once a game. Usually the alternative interpretation is brought on by the simplest of jokes, which inevitably snowballs.
Being a Shared Universe comprised of several handlers with unique personalities and outlooks, Survival of the Fittest has this in spades, often with even the people on the same side of a debate having different views. For example, there's debate as to whether Danya is a Magnificent Bastard or just plain bastard. The idea that Anti-Hero Hawley Faust's role is as a symbol of what Adam would be at the end of the game is also popular and controversial.
Tales of MU encourages this, including having a Spin-Off that gives a completely different view of some characters and events. Every major character and most minor ones seems to spark competing theories. Is Mackenzie Blaise a Mary Sue, an unrepentant sociopath, of just a normal girl who happens to be Cursed with Awesome? Was her grandmother's treatment of her horrible child abuse or going above and beyond the call of duty to raise a dangerous child? Is everything Amaranth's fault after all?
The Silver Order from Tasakeru. Are they really Good-alighned Paladins devoted to the Life Goddess, or fuzzy Nazis?
Today I Die: The young man who appears at the end of the game. Does he provide the Power of Love, or is he the reason for the main character's problems? It's subverted in that the player essentially chooses his role in her life.
Occurs quite a bit in the Whateley Universe. Tansy has a thread on the forum devoted to her that is filled with this, Jobe tended to be argued a bit before he got his own story (And possibly after), and quite a few of Team Kimba has people in canon trying to look at their actions. Also, Razorback and Mega-Death had these a bit. One was a murderer and the other is a psychopath...but both are actually really nice guys with mental illnesses. (Razorback has Hulk-style raging, Mega-Death has Diedrick's, which turns him into a rampaging super-villain. But he's actually pretty nice when not dricking out!)
Normally averted/subverted by Word of God, however. (And focus stories.)
The question on whether the characters are Mary Sues, on the other hand...
In Welcome to Night Vale, most interpretations assume that Night Vale Community Radio host Cecil is sincere about pretty much everything he says on the radio, including all of the patent BS handed to him by the town's demented government and the station's corporate sponsors. However, some interpretations go darker and assume that Cecil's aware on at least some level that things aren't right and he's being fed lies, but in order to stay alive he can't be seen to openly question them too often. Supporters of this interpretation note that Cecil will continue to talk about recently banned topics like the Dog Park right up until the Police, the Council, or Station Management start breathing down his neck. Yet a third interpretation is that Cecil's mind is what makes Night Vale's weirdness real.
Episode 36, "Missing", proves that the "more aware than he pretends" interpretation has some truth to it, although it's still not clear how much Cecil is hiding behind his perky-but-clueless facade.