Angel Beats!: It's strongly implied that a number, if not all, of the SSS members have a Dark and Troubled Past. In fact, it's implied to be a requirement to enter the afterlife.
As a child, Yuri witnessed her three younger siblings' murder at the hands of a gang of robbers. This is the root of her anger towards God. It was also her "fault" that they died because she couldn't find money in the house to give to the robbers. They probably would've killed them all regardless, but that doesn't really help Yuri's feelings of guilt.
Iwasawa had to deal with a drunk father who continually fought with her mother. She died from a cerebral contusion, caused by her own father who bashed her in the head with a beer bottle.
Hinata botched an easy catch during a critical baseball game, causing his team to be eliminated from the regional championships.
Naoi has continually lived in his brother's shadow for years and was forced to take his place when he died, leading to a serious identity crisis.
After regaining his memories, Otonashi's revealed as having one. He had an ill sister who was his only reason for living. Until she died, he carried on in an apathetic manner towards the rest of the world. Then he decided to make a difference in the world, started caring a lot more, and was on his way to medical school when the train he was on crashed and he died.
Angel has a lesser example, but her rank as Student Council President was taken away, the teachers and students have lost all respect for her, and her comfort food was taken away from her all because of the SSS's actions. It's also sad when you realize that Angel probably is a human like the rest of SSS and was just trying to fulfill her duties as Student Council President. Her reputation and life in the after world is ruined because she was trying to play by the rules.
Attack on Titan takes place in a Crapsack World and involves members of a Redshirt Army that fight Man-eatinggiants called Titans. Most of the human race has already been devoured to the brink of extinction, and the survivors live within a walled territory where the threat of food shortages and civil unrest threaten to finish them off. The characters that didn't start out damaged quickly develop issues, thanks to the constant threat of being Eaten Alive and having to watch their comrades die brutally on a regular basis. Anyone that isn't at least hinted to have some sort of emotional problems probably didn't live long enough to be developed or suitablybroken. And this doesn't even start on the Titan Shifters, who at least one of which has actually gone crazy, and they all are implied to have something seriously wrong with them that caused them to try and exterminate humanity.
The Allies are not well. England had no friends, and was bullied and hated as a child by his own family, and ends up being left by the one person who ever showed him any love. France's implied love was murdered by his own charge turned enemy. China's former little brother stabbed him for seemingly no reason and declared war on him. Russia was raised by General Winter and endured through several things that messed him up completely (Bloody Sunday, anyone?) The only one who appears to have gotten it easy is America. And when you take into consideration how The American Revolution must have affected him as well, even that's debatable.
The Soviet Union also qualifies. Russia is an insane type 3 Stepford Smiler with an awful past. Belarus is a Yandere who wants to get married to Russia. Ukraine is a sentimental girl who's always trying to defect. Lithuania is The Woobie, complete with scars presumably inflicted by Russia, and is in unwavering love with Belarus, who always abuses him: the one time he had a "date" with her, she ended up breaking his fingers, still doing so as he talked to Poland afterwards. Latvia is the fragile one who's always trembling. Estonia seems to be the Only Sane Man, but that could be just because he gets so little screen time; he's still terrified of Russia and identified as part of the "trembling trio" with Lithuania and Latvia.
It's fair to say ANY character in Hetalia fits this. Considering the fact that the cast represents countries and their histories, and that history is far from perfect, the trope is extemely justified.
While not nearly as angsty or drama-milking as other series, there's barely a character in Baccano!! that isn't maladjusted, severely traumatized, or (most commonly) justplainnuts. You know your cast belongs on the wrong side of the crazy train when even the Only Sane Man is an orphaned, Mafia-raised teenager with the Ghost Memory of a centuries-old Mad Scientist.
Hardly anyone in Berserk is safe from this, considering what a huge Crapsack World it takes place in. Some people manage to survive and better themselves as best as they can, but for most, it's a nightmarish existence topped off by a nightmarish death. Special mention goes to Guts and Casca since the universe seems to have had it in for them ever since the two were born and it really messed them up bad.
Black Lagoon. Seriously, you know you're dealing with one fucked up group of people when the least emotionally unstable characters are a Vietnam Veteran(or so we think) turned pirate-mercenary (Dutch), a jaded former police detective turned underworld kingpin (Mr. Chang), a Soviet commander sent one too many times into Afghanistan who took her troops and formed the syndicate Hotel Moscow (Ms. Balalaika), a Japanese salaryman whose life just got turned upside down (Rock), and a man who was forced to flee his home country after pissing off both the FBI and The Mafia (Benny).
The TV Series of Black★Rock Shooter. The only sane person out of the cast is Yuu. Nope. Actually, Yuu vanished into Otherworld years ago. The person we've been seeing named Yuu is actually her Otherself Strength. She's not crazy, however, she IS the crazy.
Psychologically stable people don't have Otherselves; they can stabilize, but you had to be psychologically abnormal at some point.
Bleach has large amounts of characters with tragic or complicated pasts. All six of the manga's heroes (Ichigo, Rukia, Orihime, Uryu, Chad and Renji) all have dead relatives or loved ones with different reactions to their losses which affected their lives. Other characters have had sad backstories like Matsumoto, Gin, Tosen, Ulquiorra, Starrk and Lilinette, and everybody affected by Aizen's action 101 years prior to the manga's main storyline.
In Bokurano it's rather difficult to name a major character that doesn't have issues of some sort.
Chrono Crusade isn't quite as bad as some of the other examples, but that may be in part because the original manga is fairly idealistic. Chrono was found by Rosette and Joshua Christopher sleeping in a tomb—which is later revealed to have been the final resting place of Mary Magdalene, a woman he was in love with, that he accidentally killed during a fight with Aion. Rosette and Joshua's parents are dead, and when Joshua gets Chrono's horns from Aion and puts them on his head he goes insane. Most of the people Azmaria has ever cared about have been killed or have abandoned her because of her powers. Satella's family was killed in front of her by a demon without horns, and she has spent her entire life searching for him so she can enact her revenge. Fiore is an Emotionless Girl that is later revealed to be Satella's dead sister, turned into a "mindless doll" by Aion to further his goals. Remington in the anime is some sort of fallen angel and in the manga was turned into a half-demon half-human thing by the Elder at his own request. Oh, and he may have been in love with Mary Magdalene too. In the manga, the bad guys don't even get away without tragic backstories—the Sinners are a Breakfast Club.
In CLANNAD, nearly everyone has a problem or several, some pretty bad and some not as bad as others, but nonetheless, played and displayed depressingly at times.
Same goes for Kanon and Air. Key seems to like this trope...
In Code Geass most major characters have some serious problems, which places them past the Despair Event Horizon and sometimes leads to their dragging others close to them down in the undertow. Most especially, all characters tied to Geass are seriously messed up.
Count Cain has hardly a well-adjusted character in the whole bunch, mostly driven by Cain's Big Screwed-Up Family (Cain himself regularly beaten and told he was inherently evil due to his name, his half-brother hidden in girls' clothes to keep him from a similar fate— unsuccessfully, as he was later subject to similar abuse, tricked into eating his pet, and considers other animals infinitely superior to humans— his father and mother being siblings), but also present in the unrelated and side characters. Riff seems to have some identity problems which come to a head in the climax where it turns out he's an entirely inventedSplit Personality of a cruel man working for Cain's father, Oscar developed a bizarre fixation on Cain because he resembles his dead fiancée— a fixation he then transfers to Cain's ten-year-old half-sister, and one-shot characters include a little boy who gets violently protective of the elder sister he claims to hate, a girl who was crippled by her mother so she could never leave home and who learned to kill people and preserve them so they'd never leave her. And that barely scratches the surface. At least little Merriweather seems to be okay....
Good Lord, Cowboy Bebop. Not just all of the main characters have issues, but practically everyone they meet in the entire series. It doesn't help that the theme is practically a deconstruction of Growing Up Sucks, as is fully explored in some literary papers. (Yes, you heard me; literary papers have been written about Cowboy Bebop.)
Anyone in Elfen Lied who wasn't already murderous, emotionally traumatized, or unlucky in love sure became one (or all) of those. The only character to come across as somewhat well-adjusted would have to be Nana, and sometimes, not even her!
When the most normal person in your cast is the one with no arms or legs, expect some serious issues.
Fruits Basket. In most cases if the parents of a Sohma member are mentioned, at least one rejected their child as a monster. All of the characters have at least one other tragic aspect: Yuki was abused as a child, Kyo was looked down upon as a monster even by the other Zodiac members and blamed by his father for his mother's suicide, Hatori lost part of his sight and erased the memories of the woman he loved, Shigure was involved in a twisted love triangle, etc, etc... This includes Tohru and her friends. Although at one point it was actually subverted. A flashback to Kimi being teased in middle school has girls asking why she doesn't just hang out with the guys and get by on her looks; her response is, "So you think so too?!" with giant shiny eyes and a "Big ego boost" Unsound Effect.
The Fullmetal Alchemist universe seems to have psychological trauma as one of the qualifying factors for a commission in the Amestrian military. Notable cases are the Elric brothers, who were abandoned by their father, and sparked the plot by trying to use forbidden alchemy to resurrect their dead mother. Other characters partying in Trauma Conga Line include Roy Mustang, Riza Hawkeye, Winry Rockbell, Van Hoenheim, Izumi Curtis, Tim Marcoh, and Scar. Plus, Alex Armstrong and King Bradley make the list unexpectedly.
And then the plot happens. Almost every single major character (and definitely every single major character who already had past issues) gets badly traumatized at least once by the end of the series. Those that survive will surely have issues for years to come. Earn Your Happy Ending indeed.
Truth in Television for an army that just finished committing genocide. Under the circumstances, anyone without severe Post-Traumatic Stress Disorder is almost certainly a sociopath - like Kimblee.
Most of the characters in Get Backers have some kind of personal or family tragedy that lets them lapse into angst at some point. Wangst is generally avoided because they're all huge dorks that can also lapse into shameless perversion, immature name calling, fistfights, etc. at a moment's notice.
The new Original Seven of GUN×SWORD. This is kind of funny, in that Gadved, the Only Sane Man, boasted to Van about how powerful they are and how well they work together. With the likes of Carossa, Fasalina and especially Wo...
The protagonists are also something like this, especially when you count Ray.
Which is ironic, since Seras lampshades the dysfunction.
Which is even more ironic when you take into consideration that Seras is one of the sanest characters in the series, despite having every reason not to be.
"Makes you wonder if anybody normal works in this place..."
Kagerou Project is chock full of this. There's the bastard child whose father burned down their house and her older sister sacrificed herself to save her. After she survived the fire, she gained an ability to become invisible, got thrown into an orphanage and was called 'Ghost' and 'Monster' behind her back. And that's not going into what happens later. She dies. Multiple times.
Just one example? For god's sake, this series is a World Of Woobie. How about Seto who hated his ability because A Mind Is a Terrible Thing to Read? Kano, who was actually the only one to know what really happened to his sister and had to keep it a secret to protect his siblings? Heck, Ayano herself, a heroic Well-Intentioned Extremist who sacrificed herself to save her siblings and friends, falls into this too. And the icing on the cake? They all die anyway. Multiple times.
And what about the rest of the cast? Shintaro, who had always been disillusioned with the world to begin with because of his intelligence, became a shut-in when Ayano died and in one route killed Ene and himself. Takane finally realized her feelings for Haruka and rushed to tell him, but she died before reaching the hospital. When she saw Haruka again, he had become Konoha and didn't remember her. Mary watched her mother die and lived alone for over a hundred years. Shintaro's sister Momo was the only one to shoulder her family at age 16. Hibiya watched Hiyori die multiple times in extremely Nightmare Fuel-ish manners and still suffered trauma over that memory.There Are No Therapists, indeed.
The latest group of antagonists in Kenichi: The Mightiest Disciple, YOMI (the disciples of YAMI), are all pretty messed up teenagers. Among them are a guy who was bought from a child slavery ring and put through Training from Hell that rivals Kenichi's, a prince who was Lonely at the Top his whole life and developed into a royal Smug SnakeJerkass as a result, a military nut obsessed with following orders to the point of suicide (possibly a Child Soldier as well), and Odin, whose sole motivation for becoming a vicious fighter was losing a childhood squabble with Kenichi over a badge. This is all before YAMI molded them into killing machines. Half the reason Kenichi is able to eventually triumph against all of them is because unlike them, Kenichi is not ''batshit insane''. Due to their issues, the YOMI members tend to have a Villainous Breakdownin the middle of the fight when confronted with Kenichi's conviction and/or his unexpected strength, allowing Kenichi to beat the crap out of his otherwise superior opponents.
Kodomo no Jikan: Rin, Kuro, and Mimi all have really serious issues (especially for 9-year old girls) and could definitely use some counseling. Later in the series it becomes clear that they aren't alone. Rin's caretaker Reiji's a mess for a long time ago (he doesn't seem to understand why Aoki is so squicked by his Wife Husbandry plan), Shirai-sensei has mother issues and is emotionally stunted, and Kyoko has issues (there's a reason she always wears the same sweatshirt and sweatpants ensemble to school everyday). Aoki is the only major character without any serious angst in his past. What the main storyline puts him through makes up for it.
It seems that in The Kurosagi Corpse Delivery Service's world, becoming an orphan correlates with gaining weird skills or powers. So far, with the exception of the main character, all of the main cast and a few secondary characters who also have supernatural powers have revealed that something horrible happened to their parent or parents as a child.
Kyouran Kazoku Nikki has every character coming from a dark past. Yuka and Chika suffered abuse at the hands of their family, Teika is a survivor of the near-genocide of his people, Hyouka is a killing machine suffering from humanity issues, Ouka has no recollection of his past...
Every Loveless character who isn't a psychopath or sociopath has been through emotional hell. Ritsuka (amnesia, ongoing physical abuse from his mother, the death of his beloved older brother, and the discovery that said older brother is a murdering psychopath who faked his own death) and Soubi (orphaned, raised by a teacher who wanted to exert complete control over him and sexually abused him, and physically and emotionally abused by Seimei, who saw him as an object), are probably the worst off, but Yuiko is a victim of bullying, Natsuo and Youji felt neglected by their creator, and Kio is estranged from his daughter and has been disowned by his family, just to name a few.
The title's rather apt.
The primary members of the cast in Mahou Sensei Negima! tend to have the most horrible backstories. Negi's never met his parents, is too self sacrificing and had his village burned down. Asuna was a weapon and was forced to cause the destruction of Ostia. Konoka is fairly normal, but she's been estranged from her best friend/love interest for years. Setsuna was cast out of her tribe for what is strongly implied to be albinism. Evangeline has had people trying to kill her her entire life. Chao, Rakan, Chachamaru, Anya, Kotaro, Shiori... But don't worry, not everyone is like this; Makie can't think of any worries.
Mirai Nikki. The whole cast is Ax-Crazy, especiallyYuno. The main cast is comprised of a serial killer, a terrorist bomber, a prophetess of a self-proclaimed Religion of Evil who was also used as an unwilling sex toy by them in the past, a blind vigilante ruled by his own brand of justice, a Tykebomb who suffers from elitism, a Corrupt Cop, a man who is maniacally in love with his dogs and neglects his family, the local mayor who has Nazi-like views on how to evolve humanity by giving his citizens the power of the Future Diaries, and the lead Yukiteru Amano eventually snaps after certain incidents that force his hand all the while guarded by his Ax-CrazyStalker with a Crush Yuno. The only sane characters are Yuki's friends, two diary owners who have a more stable relationship than Yuki and Yuno, and a careworker who has no interest in winning but her orphans want her to become God to make the world better.
The original Mobile Suit Gundam started it for the franchise with the White Base crew. The main character Amuro's parents are separated due to his father's decision to emigrate to space. Now he's a Child Soldier with a rapidly developing case of PTSD on top of his pre-existing issues with social contact and his father is missing while his mother refuses to accept that he's a soldier now. Frau Bow's family was killed in front of her in the first episode. Mirai has an Arranged Marriage she wants no part of, along with more deceased parents. Sayla Mass's parents are dead and she's actually living under a false name because of her father's politics. Hayato has a massive inferiority complex from being constantly overshadowed by Amuro. Captain Bright's a cadet who only winds up in charge because everyone else is dead.
Mobile Suit Gundam Wing is full of them too. Heero is orphaned very young. He's used as an assassin and trained as a child soldier. Duo live on the streets with other kids and steal to stay alive. He ends up in a orphanage and all his friends are adopted except for him. OZ and the Alliance then massacre everyone leaving him the sole survivor. Trowa is trained as a mercenary with no memory of his lost family. Quatre has a low esteem of himself and thinks his father doesn't love him because he was born as a test tube baby (in reality he was conceived naturally and doesn't know it). Wufei lost his wife during an OZ attack on his colony. Zechs lost his parents during an Alliance invasion and had his pacifist homeland conquered. Even Relena swings between this and Wide-Eyed Idealist. And then one has to wonder how Lady Une ended up with a Split Personality. Thankfully, two of the secondary characters (Sally Po and Lucrezia Noin) manage to stay level-headed and tend to steady the others whenever they cross paths. There's also, if you think about it, Treize; his status as a Magnificent Bastard actually has a stabilizing influence because he carries an imperturbable air about him that makes men rally around him.
Most of the main characters in Nabari No Ou have either a horrible traumatic past, or a horrible traumatic present. Or both.
Nana has most of its main characters dealing with Parental Abandonment, abuse or even just everyday love life issues. Drug addiction also starts to figure into the story as well.
Narutaru. In the entire 2500+ pages, there are two (one of whom appears for about 15 pages before being killed off) characters who are not broken or insane.
Most of the characters in Naruto that get any screen time usually have suffered through the death of a loved one or some kind of abuse, including Sasuke, Naruto, Sakura, Gaara, Iruka, Kakashi, Sai, Hinata, Neji... you get the point.
To elaborate: Sasuke has PTSD, among other issues, Naruto hides severe depression, Sakura and Karin have downright abusive relationships with Sasuke (read: they continue to be smitten with him even when he tries to kill them), Kakashi has a serious case of survivor guilt on account of witnessing two suicides and being unable to save his mentor or his best friend, Hinata has an inferiority complex that causes crippling shyness, Gaara had severe depression from his years of persecution at his own father's hands, culminating in failed suicide attempts and then homicidal mania by age twelve (fortunately, he got better), Neji tried to kill his cousin Hinata because he didn't want to be her slave, Sai was trained to be an emotionless killer, including being forced to fight the guy he had come to regard as a brother to the death. Let's not even get started on the villains...
Neon Genesis Evangelion. Good God. Keeping within the circle of main characters, we have: Shinji, the shy, borderline-depressed protagonist with negligible self-esteem and self-worth and a massive guilt complex; Rei, an emotionally-repressed Extreme Doormat who sees no issue with considering herself expendable; Asuka, a self-hating, abrasive, attention-seeking Tsundere borderline-narcissist; Misato, a Broken Bird who craves love and acceptance but fears more than anything the very commitment that comes with the deeper relationships said desire entails. The restof thecast islittle better. In fact, Evangelion's cast is sufficiently messed up that the viewer practically needs similar issues of their own to identify with them - and that's not a good thing. Those who don't may well find it easier to identify with a cast of Mary Sues. This is the terrible thing with mental disorders, it's very hard to imagine what the people suffering from them go through. And Evangelion depicts these disorders very accurately.
The manga version (written by character designer Sadamoto) features a much less screwed up cast. However, Evangelion is technically Anime First; the manga was initially only made to stir up interest. This being Evangelion, there's still plenty of dysfunction to go around.
Rebuild of Evangelion introduced some positive properties to each of the main cast: Asuka is willing to be nice to others, Rei gradually comes out of her shell due to her crush on Shinji, Shinji himself demonstrating more bravery and self-assertion... and yet, Evangelion 3.0 manages to break the characters either on screen or inferred, with the Fourth Impact
Now and Then, Here and There is about Child Soldiers who aren't afraid to inflict upon "enemy" villages the same horror that kidnapped them from their own (despite their latent PTSD and Survivor Guilt), rape camps stocked with Broken Birds producing future soldiers...and a literally insane warlord ruling over it all. The worst part? The director was inspired by the very real, verybrutal civil wars in Africa.
Subverted and played straight in One Piece. Subverted in that every member of the Straw Hat Pirates has a depressing backstory, but very rarely does it ever seem to get them down. Other characters, on the other hand, play it straight. Montblanc Cricket was bullied and derided for most of his childhood because of something his ancestor did (ironically, his ancestor was telling the truth and no one believed him). Boa Hancock and her sisters were sold as slaves to the Celestial Dragons when they were young, who did such terrible acts to them that they can't even speak about it without breaking down into tears. And surprisingly, Arlong and his followers presumably went through some hard times, as mermen and fishmen were always treated horribly by humans.
Oniisama e...: Everyone. And if they don't already have a tragic past, all the drama in the main story more than makes up for it.
Ouran High School Host Club might look like a flamboyant, over-the-top explosion of pure fluff, but when you get down to it, the main characters are all very heavily influenced by family problems. Haruhi struggles with confidence and identity issues because of her dead mother and cross-dressing father. Tamaki is hiding a vast amount of hurt and confusion because his grandmother hates him and his high-powered businessman father inhabits a world that runs on a different code of ethics than he grew up with. Kyoya is driven by the need to surpass the achievements of his two older brothers in order to earn the respect of his father. Kaoru and Hikaru are so dependent on each other as twins that they are almost unable to relate to other people alone. Honey is rejected by his family because he prioritizes cake and cute things over his dedication to the family martial arts, and Mori has essentially no identity beyond helping and supporting Honey. The amount of drama all this causes is frankly astounding, and essentially runs the whole plot of a sixteen-volume manga series. Once you get into some of the plot twists, the issues get even darker and deeper. Admittedly, these are mostly pretty light compared to some other examples in this section, but still, one would imagine there would be one relatively normal character with a happy and well-balanced childhood and home life, out of seven. But no.
And then there’s the minor characters: Nekozawa, who is obsessed with black magic and death and cannot come out in daylight, and his three-year-old sister who developed an addiction to explicit shoujo manga because she cannot interact with her brother, being terrified of the dark.
Pandora Hearts. It'll be hard naming a character that lacks any issues. And the protagonist is far from safe.
Madoka is a shy little girl who has no self-worth and feels useless, which enables her to delete herself from existence to save the world.
Sayaka is a stubborn loudmouth with an unwavering devotion to justice that leads to her eventual transformation into a witch, as she refuses to replenish her Soul Gem because she thinks it's unheroic. She ends up broken and alone after watching her best friend fall for her crush and having her life destroyed by her wish.
Kyouko is a harsh, selfish Social Darwinist who won't kill familiars until they kill several humans and evolve into witches capable of dropping the Grief Seeds she needs, thinks Sayaka should win Kyosuke's love by breaking all his limbs and rendering him helpless without her, and watched her father commit a murder-suicide on her entire family after her wish goes horribly wrong.
Homura is the queen of dysfunction. She watched her only friends die multiple times while desperately trying and failing to save them through her "Groundhog Day" Loop powers, which eventually became so traumatizing that she abandoned all emotions and went from being a sweet little Moe with glasses and braids to a cold, hard Badass who fights with an armory of guns and bombs she stole from the Yakuza. Every time the time loop resets, she has to watch Madoka, whom she's relived a single hellish month over and over to save, as well as the rest of the cast, shy away from her in fear and treat her like she's an intimidating stranger. Once she proves herself to them once again, they die or transform into witches. Eventually, with her help, the circle is broken and her best friend becomes a goddess that no one but Homura remembers, and leaves her Walking The World alone with the promise to come for her when she is about to die. Even then, she perseveres and soldiers on - and then the Incubators try to prevent their reunion and use her as a bait to strip Madoka of her powers. This is when she breaks and takes said powers for herself instead in order to punish the Incubators and grant everyone else a normal happy life - and keeps hating herself throughout for this act of betrayal, deeming herself an irredeemable God of Evil.
Kyubey can't feel emotions - in fact, his species regards feelings as mental disorders. Considering what happens to every single one of his recruits, it's not like this conclusion is misplaced.
If a character in Rave Master didn't lose their parents at a young age then they either lost something worse or don't get to be part of the main cast. Bonus points for Musica, who loses his whole family as a little kid (to an early villain) and, several years later, loses his adoptive father to disease. And no, the bad guys aren't immune, either. In fact, the Raregrooves are bad guys because the universe keeps messing with them.
Revolutionary Girl Utena: Everyone in the series has a closet packed full with skeletons. In one of the earliest examples, Nanami killed the kitten that she had given to her brother as a gift only days before because it was taking his attention away from her. And she was just a little kid at the time. Compared to other characters in the cast, that's quite tame, actually.
The majority of the main characters from Sailor Moon fill this trope: two characters were orphaned at an early age (Makoto even lives alone as a minor), two have dead mothers, one is the child of divorce, and three never have their parents mentioned at all. Only three of the main characters have whole nuclear families (incidentally, these are the happier, more-or-less well-adjusted characters) and both ChibiUsa and Minako have some intense issues with their parents—ChibiUsa feels completely inferior to her messianic mother, and Minako is constantly hounded by her shrill one. Usagi's really the only one without any deep-seated problems regarding her folks.
With two exceptions, the Senshi all have lonely lives at school before they team up, as well.
Oh, Saiyuki. Much of it family-related. We have dead parental figures, sibling incest, parental incest, parents attempting to kill children, children killing parents, characters murdering entire villages and clans...
In Sakura Gari between Souma's childhood, being raped and tortured DAILY, silently and lonely while everyone pretends it doesn't happen, Matasaka's childhood and rape and torture at the hands of Katsuragi, the situation with Youya, and Souma's stepmother, Katsuragi and Sakurako and you have Up to Eleven extremes that just keep on climbing.
Oh boy, let's try to collect a list. There's the two main characters, Itoshiki Nozomu - a suicidally depressed attention seeker - and Kafuka Fuura - an optimist who pretends to be stupid to cover up her brutal childhood. There's Chiri Kutsu, a psychotic Yandere afflicted with OCD who will kill people over wearing odd pairs of socks, there's Komori Kiri, a hikikimori who ends up living in her teacher's bathroom sometime during the second season, Matoi Tsunetsuki, who dresses like her teacher, Nozomu, eats the same food as him, followed him around everywhere - including the bathroom - and checks his mail. Then there's Keare Kimura, whose multiple personalities merged into several hundreds representing national stereotypes after going to Japan (not to mention the fact that her skirt defies gravity), Abiru Kobushi, a tail fetishist who shows many symptoms of some kind of autism (deadpan, dislikes human company, somewhat shy and reserved), Meru Otonashi, a shy, quiet girl who sends abusive emails, Haruhi Fujiyoshi, a homophobic who loves gay porn, Maria, an immigrant who may or may not actually be female, and her unnamed friend who carries around a gun, Nami Hitou, whose schtick is that she has none, yet may have an eating disorder, repeatedly self harms, once tried to jump out of a third story window for attention, but is just sane enough to be completely hated and ignored by the rest of the class.. And to top it all off, Mayo Mitamo, a girl who appears once a chapter, has no dialouge or real role, just to molest a dog with a stick, Kaga Ai, who has a huge guilt complex and apologised over being born, Okusa Manami, who is marries to an abusive husband, Oora Kanoko, whose constant smile and disregard for the situation (including walking into jail during a full-on, incredibly violent brawl) and simply walking out with her teacher (it's a long story) is probably because of prolonged drug use, and two girls, Maruichi and Nezu, who reguarly do business scams together - and who can forget the self-obsessed net idol, Kotonon, along with Jun Kudou, a bookworm whose very traditional, very Christian family pretty much gave up on him, for afewreasons? And those are just some of Itoshiki's class.
School Days. The high school in the game and anime appears to be attended by people with a fairly weak grasp of reality, which doesn't particularly help the already fragile mental health of the lead characters. Like Eva for Humongous Mecha, this is used to further its Deconstruction of Marry Them AllH-Games.
Seitokai no Ichizon: Zany antics and laughter aside, everyone in the council aside from Kurimu has some deep seated personal trauma, be it bullying (Chizuru), a broken family (Minatsu and Mafuyu) or a broken heart (Ken).
Wandering Son is more mild then most examples here, but still counts for several reasons. It's mainly the main trio though. The protagonists are having troubles related to them being transgender, along with typical adolescent problems. Chiba however is just... rather dysfunctional for most of the manga, lacking proper social skills and being depressed often.
Weiß Kreuz all main characters have serious issues. Either there is a dead lover, a little sister in a coma, a backstabbing friend, or a whole family of psychothic people; rest assured that these bishonen are scarred for life.
Everyone in Welcome to the N.H.K. has either a tragic past or a tragic present. In detail: Satou is psychotic and scared of strangers; Yamazaki found out just before the series started that his parents had planned his entire life out for him; Hitomi is also psychotic with a particular bent toward conspiracy theories and seems to also be depressed; and Misaki, leading the pack, well... her father is dead, her stepfather was abusive, her mother may or may not have committed suicide, and she herself tries to commit suicide due to delusions of inadequacy caused by said abusive stepfather. On top of that, she also has borderline personality disorder.
Misaki is even worse in the manga, where That entire history is made up to garner sympathy and attention. She even did the cigarette burns herself!
White Album. Touji is a slacker and seemingly can't take any kind of initiative, Yuki is an Extreme Doormat, Yaoyi is... well, not particularly functional, Haruka seems to be something of a Wild Child, Misaki can't function, Mana is neglected by her parents, Eiji is... Well, just crazy. All in all not the most mentally stable of casts.
All the important characters in Wolf Guy - Wolfen Crest have rather significant problems. Those who currently have manageable ones will undoubtedly have more piled on top of those.
Every character in Yu-Gi-Oh! has either a tragic, depressing backstory or present.
Every member of the cast of Yami No Matsuei (aka Descendants of Darkness,) has some sort of horribly traumatic past. It seems to be a job requirement for shinigami. When one of the protagonists, who suffers from a cripplingly uncontrolled power of empathy, to say nothing of the ancestral curse, combined with a childhood spent locked in a cell in the basement and a sibling who shares his given name and was murdered by their parents, and ends up being raped and murdered via a wasting curse cast by the main villain all by the ripe old age of sixteen, and his backstory is comparatively cheerful next to that of his partner... well, it's just a pity that the department is run on too much of a shoestring budget to hire a staff therapist. They could use one.
The majority of the villains in Yu-Gi-Oh! GX have a Freudian Excuse, and given the series usual penchant, this is probably intentional. Then there's the Protagonist, Judai, who is far by the most mentally screwed up character in the series, and he only gets worse as time goes on.
Examples of villains can be summed up in 4/7 of the 7 Stars. Camilla is a vampiress whose people have been killed by humans and took refuge in a coffin until Kagemaru found her. And Abidos III rebelled against his advisers over dueling. However, the worst cases are for Darkness and Amnael, better known as Asuka's older brother Fubuki and Daitokuji-sensei. Fubuki mysteriously vanishes in the abandoned dorm one night and became Darkness. And as for Amnael's origins... Daitokuji was an alchemist. Kagemaru funded his research, but Daitokuji fell gravely ill and had to make a second body to continue. And it turns out all along that Daitokuji wanted to stop Kagemaru.