It can be surmised that Tsuruya has been raised to be Depressed from the first chapter of the Initial Conflict arc of Kyon: Big Damn Hero.
Children of an Elder God: In chapter 22, Asuka tries to smile when her friend Anna tries to comfort her, but it was plainly visible that she was still in pain.
In ''The Demon's Contract", Kasumi Tendo is deeply broken from being forced to be the caretaker for her family since she was nine years old. While everyone reacted normally (for them) to Ranma's rampage before he goes back in time, Kasumi simply kept on smiling, even when Ranma explicitly said he was going to kill her. After he used pressure points to break down her mental barriers, Kasumi cries, curses, and breaks everything in sight before taking it out on the one she blames most for her life: her father.
In How the Light Gets In, Laurel has been suffering from chronic depression, addiction, and an anxiety disorder all her life, so all her smiles have shades of this. A specific instance of this happens at the end of chapter 3, where Dean notes of her smile at Oliver:
"It's one of those soft, sweet, unwaveringly kind smiles of hers meant to comfort. Dean knows these smiles of hers well. About half the time, they're a lie. She uses them to draw people's attention away from her trembling hands. She was so irritated when they stopped working on him."
In the fanfiction Composure, Princess Celestia is so trapped in her own image of composed benevolence that she breaks when Luna attempts to get her to acknowledge her feelings, releasing a millennium worth of repressed emotions all at once.
Pinkie Pie can appear anywhere on the spectrum in fanfics. In The Party Never Ended, Pinkie Pie is Depressed, as she breaks under her Genki Girl cover as she dreads over her love for Rainbow Dash. As for Cupcakes, well, let's say she's Unstable and leave it at that.
Rarity is Unstable in The Killer Rarityverse fic The Secret life of Rarity, in which she maintains her social life over a period of 16 years in which she murders over 100 ponies/other races. She starts to slip towards the end, leading to her confrontation by Applejack.
Ash in Pokémon Reset Bloodlines is a downplayed example. While he's not secretly wallowing in despair, he has his moments, especially when he's reminded of something he lost from the original timeline, and he can't share his pain with anyone else but his Pokémon.
Implied to be the case with Reimu in Gensokyo 20XXV, as it is found out that not all her smiles are genuine, actually, she smiles out of acceptance towards her situation and to comfort everyone else.
Ren: [...]If anything her smile is her way of comforting others and herself mostly, diverting attention away from her sorrow and pain, much like how Chen purred to herself.
Delaney Pollack of Fargo acts like a cheerful Proper Lady when the cameras are on, but beneath that persona she's a cruel, stab-happy sociopath. Later chapters imply that's an act too, and that the real Delaney is actually a contemplative, distant Emotionless Girl. Her persona in the afterlife suggests that the latter interpretation is the most accurate of the three.
In A Charmed Life Light is very emotionally stunted so while he thinks he's alright in reality he is actually quite miserable. Ryuk and L are the only ones to ever figure out what's Beneath the Mask and Ryuk is the only one to never judge him for it.
Light: Class ended and before I could even move from my position, females (if they could be called that) flocked my surrounding table. It was utterly disgusting. I casually said a pleasant goodbye to Ryuzaki before being escorted off to the library to help out a fellow classmate. I would rather slit my wrists and write my own name in the Death Note, but sacrifices had to be made to maintain my identity as the perfect individual.
But he got it now. He got what everyone was looking for. It wasn't for him to be happy, and he wasn't trying to be mean thinking about that. People wanted other people to fit into a nice, neat package with smartly tied bows that were the right color to match the wrapping paper. People wanted to be able to classify other people, and for them to behave according to code.
Light found his code.
His role is son, older brother, protector, student, genius, role model, kind, earnest. His role is to be perfect so they don't have to worry again, so they won't say he's abnormal, strange, worrisome (all whispered in the dark night across the kitchen table when they thought he was asleep).
Draco Malfoy often gets this treatment in sympathetic fics that don't actually put leather pants on him. I.e., he's spent his whole life trying to be what his father expects him to be and has no idea what he is. More of a Stepford Smirker, of course, but it's entirely possible he does smile at people who aren't Harry Potter and his friends; we'd never know.
In Amazonian AWOL Blaise Zabini does his utmost to maintain a cheerful front despite the fact that his ex-wife is draining him dry financially and he's on his last chance with his boss.
In Laughing not only is Harry depressed but Ron and Hermione are helping him keep up the pretense.
In The Lily Potter Foundation Harry's been depressed and hiding it for much of his life, thanks to his abusive relatives and the indifference of the wizarding world.
In Wear Me Like a Locket Around Your Throat Orion Black nearly always maintains a cheerful, happy-go-lucky demeanor despite his dysfunctional family, the slow death of his younger brother Rigel and an unwanted engagement to his cousin Walburga.
Invader Zim fanfics about Keef are pretty rare, but those that exist often portray him as having neglectful of abusive parents. Given Jhonen Vasquez' style, this is entirely plausible (compare Squee!, for example.)
In the Captain America: The Winter Soldier fanfic Out Of The Dead Land, Bucky starts out as one: he memorizes information from history books, carefully parrots details of Steve's stories of their youth back to him, and even practices his facial expressions in the mirror to act as the good-natured, easygoing best friend Steve remembers and cover up the fact that he doesn't actually remember anything about his past. It works for a while, until Natasha exposes his act.
In the few fics that actually center around and/or care to develop Big Macintosh he's generally portrayed as being Depressed or Empty for one reason or another. Hinted at in the example below, from the heretofore-unfinished shipfic "Like I Imagined":
Applejack glanced at her friend. "Usually he's just all plain an' sleepy-like, but sometimes he gets this look on his face like..." "Like?" Rarity echoed. "Like there's a bunch a' gears workin' in his noggin." Applejack frowned. "An' I don't much think I'd like to know what they're puttin' out." "Why not?" Rarity looked over, concerned. "'Cause when he gets like that, he looks darn near fifty." The earth pony shook her head. "It ain't right for a colt to look twice his age."
Though it's just as common for the "idiot facade" to be the only thing keeping him sane from the abuse he receives from almost everyone (which is usually a lot harsher than canon, with mobs beating him and sometimes even being raped).
"Most shinobi tend to go for the unnoticed and low-key approach, they strive to be dismissed as nothing. A rare few do the opposite; they exaggerate and posture so much that an observer cannot see the truth. I believe Asura is fundamentally a person who finds it difficult to be anything less than himself, so subtlety is not an option for him." "So, what you're saying is –" "It is just another type of mask. But it is also not necessarily all false."
'Til You Feel It All Around You reveals that Usopp was already developing into one of these at the tender age of seven. At one point, when Sanji affects a false cheer to try and reassure his temporarily deaged nakama, Usopp shows him how to 'fix' it and smile more convincingly. Sanji's rather freaked out by the demonstration.
The AU series Sith Academy initially portrays young Obi-Wan Kenobi as pathetically cheery and happily co-dependent in a rather sick relationship with Qui-Gon. It eventually got to be too much, so authors decided to explain his demeanor as the result of a super-Prozac drug called Perkium, that was being used to medicate the formerly rebellious punk padawan into perfect Jedi conformity.
The Conversion Bureaudeconstruction fics (with some implications of this in a few straight TCB fics) paint the Newfoals (humans transformed into ponies) as Empty with some elements of Unstable. Details vary from fic to fic, but most commonly they can't feel negative emotions, can't swear, and have changed from their human personality so much that it's just not the same person.