Winnowill of ElfQuest is smiling and regal, pseudo-friendly and aloof -when she's not getting her kicks torturing Strongbow or messing with other elves' heads.
Both Yubiseiharukana Tanaka and Sara Matsunaga from Ever17 - the former has a terminal disease and works at the LeMU theme park to support her cloned daughter, while the latter has been subject to bullying and illegal scientific testing for years, to the point where being trapped in a sinking theme park, away from Leiblich's clutches, is actually why she's happy.
In Tsukihime, the maid Kohaku is this for some very very dark reasons.. This trope is lampshaded by the main character when, while comparing a No So Stoic character whose emotions were palpable behid the unflapable exterior with the perpetual smile the spoilered character showed, said something in a vein of "showing only one emotion may be the same as having no real emotions inside".
In Little Busters, Haruka is a Type A, using her cheerful energetic personality to cover up her depression and crippling insecurity. Komari also becomes a very creepy Type A whenever she encounters something that triggers her memories of her dead brother, causing her to Heroic BSOD. At first she's just depressed, but when she starts repressing her memories by pretending another person nearby is her brother, she starts acting just like everything's normal again - except for her dead, cold eyes...
In Umineko: When They Cry, it turns out this is the case with Shannon of all people. The cute and clumsy Meido is simply a Split Personality/Imaginary Friend of a person known only as Yasu, who is the one who orchestrates the murders with his/her other personas Kanon and Beatrice because s/he couldn't find a solution to being in love with three different people (George, Jessica and Battler). Battler's sudden return after six years only adds to his/her madness. However, it also turns out the horrible, cold blooded murders she commits on the gameboard aren't quite what really happened on Rokkenjima. The murderer in the real world is heavily implied (though never outright stated) to be another Stepford Smiler, Kyrie.
Emi Ibarazaki from Katawa Shoujo. She is cheery, energetic and happy-go-lucky as they come, but it's really a facade to cover up the trauma of losing her father in a car accident in which she also lost her legs, as well as the fear of losing the people close to her just like she lost her father.
Shiina "Misha" Mikado is also a cheery and playful girl, but it's becoming clear late in her route that it's a an act to cover up the pain of Unrequited Love after Shizune rejects her confession. Lampshaded by Shizune in which she said this:
Shizune: The Misha you know is different from the one I think of, when I think of the time we first met. Even though I think she looks better cheerful and smiling, that isn't how she typically is.
Sayaka Maizono in Danganronpa. Even though she seems to be a cheerful Idol Singer at first, she is the first student to crack under the pressure of Monobear's game, which led her to attempt to kill some students and frame Naegi for that. And she also has a crippling fear of being forgotten and abandoned which stems from her workaholic father and always being alone which is why she became an idol singer so she get the love and attention she desperately wanted.
There's also Celestia Ludenberg/Taeko Yasuhiro as a Type C. She seems to be smiling and even accepts that she is locked up in the school forever so easily, but she is actually lying the whole time and she even tries to implicate a student for the murders she caused so she can escape from the school, collect the bribe money and to fulfill her dreams. Naegi implies that, nearing her execution, she becomes a Type A, meaning that she fakes her smile to show that she's scared of dying.
CLANNAD: Tomoya Okazaki is a Type A. The casual behavior might fool the watcher/reader for awhile, but it becomes clear over time that he's basically starting the story in despair.
An oddly non-creepy example that doesn't fit into any of the categories is Ambassador Colias Palaneo in Ace Attorney Investigations, who mainly keeps a constant smile as part of his ur-politeness. The fact that he drops it pretty easily helps out.
Kristoph Gavin is a villainous Type C example: a Machiavellian madman who hides beneath a mask of contentment and composure.
Add Souta Sarushiro to the list of Type C villains.
Though also give him a slight Type A as well. After all, living most of your life assuming your best friend's deceased father was really your own father and your father was actually your best friend's father and the murderer of the man you though was your father will really mess you up.
Klavier could possibly be a Type A, seeing as he seems fine during the credits, but during the last part of the final trial was anything but.
Nagito Komaeda is a pretty solid Type A in Super Dangan Ronpa 2, at least until He starts losing what sanity he has left. His free time events in the game proper and the Dangan Island bonus game hint that this is a combination of an incurable brain disease and an incredible cycle of good and terrible luck that has left him so burnt out on everything that he just wants to die.
In Hatoful Boyfriend there is an A-type mixed with Obfuscating Stupidity in Yuuya Sakazaki. It's part of a mask of general good cheer and unflappability which he wears just about all the time; even he doesn't know just how much is a bluff. Even when dying he says he's fine.
Holiday Star reveals that Hitori Uzune as Nanaki Kazuaki is a full-fledged Type C-for-Crazy.
Mixed Gender Examples
In A Profile, Masayuki is implied to be one for a time, but it turns out to be untrue and that he really has simply changed, mostly for the better. Miou, on the other hand, is pretty emotionally damaged inside.
It's strongly implied that Nagisa Furukawa's parents, Akio and Sanae, at least partially fake their One of the Kids behaviors. They are genuinely loving and sweet persons, but they hide their own worries and sad thoughts to keep their very frail Ill Girl daughter happy, in an attempt to make up for having neglected her a lot as a little girl. It's confirmed in After Story, where Sanae tries to cheer up Tomoya by acting like a Manic Pixie Dream Girl, but can't keep up and finally cries and lets herself grieve for the deceased Nagisa.
Rena is also a perfect example of a Type A. It's all a facade, but she does it to escape from her sadness.
Rika too. To all the world she's just a Cheerful Child, because she's convinced that if she lets anyone know something's wrong they'll just get hurt, and she's given up anyways. The reality of her situation is pretty bad, and in private she resorts to drinking away her problems.
In fact almost everyone in the series can be said to be this. They are first shown a a group of cheerful persons, and indeed the first episode looks like it's gonna be Lucky Star 2. Then we find out that Rika has revived at least a hundred times after being brutally killed, and remembers every single deaths she has been through and have being doing this for at least a 100 years; Keiichi, was a loner who began shooting little girls with a BB gun when he got bored of studying, stopping and admitting his crimes when one of his victims got hurt and have been feeling remorse since then; Satoko killed her parents while under the effect of Hinamizawa Syndrome, and believing that her brother will only return if she is strong, to the point where she refuses help in the arcs where her abusive uncle returns ; Shion who lost her beloved Satoshi by Oyashiro-sama's curse and blames the Three Families of Hinamizawa for his disappearance; Rena suffered from her parents' divorce, and on top of that, seeing her mother with another man lead her to viciously wound some of her classmates during a rampage (who was possibly trying to rape her) and changed her hame from Reina to Rena in order to leave her past behind; Takano is so twisted by her horrifying past in an Orphanage of Fear that she doesn't even care about how many thousands of people will die to help her become as famous as a god. But outside of that, they're pretty happy and smiling...
Of the four main girls in Symphonic Rain, Torta, Fal and Phorni are one of these. Lise would count if she actually smiled too.
Kali Utsumi from Remember11 is kind, serene and motherly... Or, rather, she's putting up a façade to hide her sorrow from having her own son killed in a brutal spree killing, while plotting to kill one of the people she's currently taking care of - the mentally diseased girl who killed said son - and commit suicide in the process. Jesus.
Her husband, Seiji Yomogi, is a laid-back, practical, fatherly man who acts as a soothing voice of reason in times of panic when his fellow survivors are freaking out. He also happens to have a terrible guilt complex and a lot of repressed anger as a result of losing his child. When he stops being Mayuzumi's doormat and snaps, he exiles her to die of hypothermia, strangles Yuni to death, hallucinates that Kokoro is his dead son and apparently tries to rape her. While smiling all the time.