Toki's past and if they are to be believed started is this, particularly so when she tried to runaway from them and, as Brownie put it She was once sweet and only wanted to be loved. Lets see? Here they are:
She was abused and then neglected causing her to almost die of leukemia, during the events of Flashbacks I, something that caused something in her to drive her insane in the next incident (see below)
She returned to the place where she was once abused so she can get hold of the inheritance money but went insane during the events of Insanity and Resentment and has had issues eve since.
Frailine (the one Toki abused) is also an example as per these statements:
She was imprisoned for being criminally insane after the events of Little Girl's Revenge when she almost killed Toki and damaged the border between this world and the next. Kind of a Disproportionate Retribution, compared to what Toki did to her (abused her and then, sometime afterward, she sent to Alaska attached to a bus by a magnet with no means of getting home)
Sometime after being imprisoned, she almost kills herself twice and is never seen again, as per stated, in Diary of a Borderline Schizophrenic, driving Toki into more self-hate because of it.
Bunny and Madgie's parents died in an accident when Bunny was twenty and Madgie was nine.
Doki was separated from her twin sister Toki at when both were going on thirteen and was sedated and frozen.
Before leaving his home planet on the Dionysian, Fiearius Soliveré of "Caelum Lex" worked as an assassin for the dubious government organization the Society, potentially murdering many innocents. This culminated in an event that caused both his wife and four year old son to be killed.
Josephine was viciously bullied both at school and online, betrayed by someone she thought was a friend, and raised by an abusive, alcoholic aunt. This has all contributed to her present self's unhealthy sense of paranoia. Fortunately, she's since been Happily Adopted, and has slowly been working on getting better.
Zia's father shot himself when she was eight, she was bullied at school for her outsider status and acne-ridden skin, and then her mother got diagnosed with cancer and required Zia's constant care, leading to most of Zia's friends moving ahead in life and leaving her behind. She's since gained many more friends, and her mother has recovered, but she's still been left with a morbid depression that she hides behind an upbeat facade.
Jessica's mother was severely traumatised after her boyfriend and parents were killed in a bungled robbery. She sought out old flames for a series of one-night stands, which is how Jessica was born. She's spent most of her time since caring for her reclusive mother, which in turn has left her ostracized and fed into her jerkass personality.
While most of Edward's upbringing was normal, he's had to endure a slew of intense physical surgeries to help with his cerebral palsy. This has had a traumatic effect on him, to the point that he briefly considered suicide. He since doesn't try to think about it.
Daigo was the result of a one-night stand between his celebrity father and his lower-class Japanese mother, the latter of which has now passed away. He was then subject to physical, homophobic, and racist abuse by his father and step-mother, until he eventually fought back and poisoned the latter to death. His tumultuous upbringing has caused him to regard himself as a villain, and contributed to his desire to become a leader through any means necessary.
The Opening Narration of Doom House explains how the wife of the main character, Reginald P. Linux, had died long ago and that this had left a severe depression weighed heavy on his soul.
Par for the course in Fallout Is Dragons. Granted, it's set in a post-apocalyptic wasteland, but thus far two player characters are former raiders, one was abandoned by his mentor after nearly damning a filly, one was physically and psychologically tortured by his own "teacher", one was forced to kill his own brother for no other reason then to amuse the Big Bad, and one lost his memory, leg, and EYES in an explosion. And that's not even factoring in the NPC backstories...
Jeanette of Funny Business is revealed to have this in the flashback. It turns out that having omnipotent power from a young age can do a number on one's psyche.
The Nostalgia Chick had a judging mother and an emotionally distant father who both were alcoholics and yelled at each other constantly, had an uncle that molested her, got bullied at school for being the awkward dork, became an alcoholic herself and somehow got fixated on guys she could fix and control to do whatever she asked of them.
The crew of captain Icomb's ship in Skies Unbroken has: two former Sky Pirates (including the good captain himself), one not-so-former Sky Pirate who joins later, a soldier whose side lost The War Just Before, and a Waif Prophet. It's their passenger's Dark and Troubled Past that is, however, most frequently (if vaguely) alluded to.
Madiha Nakar from The Solstice War is an amnesiac orphan and is hinted at having done a lot of horrible things as a child during her country's revolutionary war, where she fought on the socialist side.
Tasakeru's primary characters, the Outcasts, are shining examples of this trope, it's pretty much a prerequisite for being one. One is a runaway Samurai suffering from Survivor Guilt, one was thrown out on the streets with her mother as an infant and grew up in poverty, and one was disowned by her family for being a mage. And that's just the ones we know about...
Touhou: a Glimmer of an Outside World has many, many indications that Yuuka wasn't quite as mentally stable as she is in the roleplay in the past. Like a basement with a room full of torture equipment.