Dark Secret

Some characters that just have some dark terrible secret in their pasts that they don't want anyone to know. Sometimes they killed someone close to them. Sometimes they're secretly a double agent. Sometimes they took the last cookie from the cookie jar. It doesn't matter how big or small the secret is, it just matters that the person keeping it thinks that it's vitally important that it stay hidden.

There are two standard reactions to these coming out. Either everyone involved is shocked and horrified and lives are ruined. Or it's almost an anticlimax either because they've known all along, or it just wasn't as dark a secret as the keeper thought it was.

When it's a whole town that's doing this it's a Town with a Dark Secret. When you get even bigger in scale you get an Empire with a Dark Secret. My Greatest Failure is a particularly common type of Dark Secret, and it is often an element of a Dark and Troubled Past or a Mysterious Past and revealed in a Troubled Backstory Flashback. Related to They're Called "Personal Issues" for a Reason. See The Not-Secret for when your secret is not so secret. When they cause you to be suspected of unrelated crimes they become the Big Secret.

This being a trope about secrets there will be Spoilers ahead.

Examples of Dark Secret include:

Anime and Manga

How Tsume got his scar in Wolf's Rain. When his old pack was attacked by humans, he ran away, leaving his friends to die because he was afraid. He was exiled, and in the process he got his scar.
Soubi in Loveless never tells Ritsuka anything about his past, especially the parts of it that involve Seimei. There's a reason for that. A twelve year old kid doesn't need to know that his beloved older brother was a sociopath who physically and emotionally abused his best friend/mentor/partner.

Film

The movie I Know What You Did Last Summer is built on a dark secret shared by a group of friends after they accidentally kill someone with their car.
- A similar secret is kept by the protagonists of Urban Legend, involving the invocation of an urban legend to scare someone, leading to a fatal car crash.
In the movie The Watcher in The Woods, a group of friends have kept the secret of Karen's disappearance since they were children, and are haunted by it.
One Missed Call has Munchausen's By Proxy as the dark secret of one character.
A Nightmare on Elm Street's Dark Secret is the decision by the parents of Elm Street to take the law into their own hands and kill Freddy Krueger, who was known back then as the "Springwood Slasher" and liked to kill children.

Literature

Zoe from Percy Jackson and The Olympians: The Titan's Curse is Atlas's daughter.
In Daphne du Maurier's Rebecca, the heroine's husband has a dark secret. She believes he can't love her because he's still thinking of his first wife Rebecca who was supposedly drowned in a sailing accident. Turns out he had murdered Rebecca himself -- and she had goaded him into it.
In the fourth Dark Tower novel, Roland's friends must see his dark secret to proceed along the Beam. They find out he shot and killed his mother, upon seeing Rhea's reflection in the Wizard's Glass.
In the first Ellery Queen novel, "The Roman Hat Mystery", the murder victim is a blackmailer. No one familiar with the rules of Golden Age mystery novels will consider "murderer is being blackmailed" a spoiler. The secret worth killing over? One of the murderer's ancestors married a black woman. The line is so diluted that there are no visible signs of African descent in the murderer's appearance, but that "drop" of blood would ruin him socially and professionally.
In the both the books, and the 90s TV adaptation of PG Wodehouse's Jeeves and Wooster stories, Jeeves reveals British fascist leader Sir Roderick Spode's terrible secret to Bertie: Spode owns a ladies' fashion boutique. Should this become widely known it would ruin his reputation.

Bertie: You can't be a successful Dictator and design women's' underclothing. One or the other. Not both.

The reader is every bit as aware of it as she is, but Gara Petothel / Lara Notsil, in the X Wing Series, is a Deep-Cover Agent who's gone through a private Heel Face Turn, and is unhappily aware that the badly damaged pilot who she's falling in love with is damaged because of her actions.
In the Warrior Cats series, many cats' forbidden relationships. The parentage of kits born to said forbidden relationships. Visiting the Dark Forest.
The Missus and John-the-dig in The Thirteenth Tale can't let anyone know there is a third girl in Angelfield, or else Charlie's rapes and incest will become open public knowledge.

Live Action TV

In the Cold Case episode The Hen House the victim was killed for discovering that her murderer was really a Nazi pretending to be a Dutch Jew.
An episode of CSI New York had the Nazi pretending to be a Jew secret. Unfortunately for him he married a Jewish woman raised his own son as a devout Jew to keep his cover story up.
An episode of CSI has an episode where a school boy with neo-Nazi beliefs is murdered. He was growing out of racism after making friends with the school's black janitor. The suspects were other neo-Nazis who not only found out, but for some reason concluded he was also in a homosexual relationship with the janitor.
Power Rangers Dino Thunder: Trent, the White Dino Ranger, is the son of Anton Mercer, a.k.a. Mesogog. When the Rangers find this, they're a bit amused.
The whole premise of Dexter. His secret is quite dark indeed...
Babylon 5, with Ivanova secretly being A rogue telepath. Sheridan also has a secret, in that he's a member of a military conspiracy to overthrow President Clark. Then there's Delenn... you know, with Babylon 5 being a Space Station Of Spies, it's safe to say that there are many people with dark secrets.
In Stephen King's Storm of the Century, many of the residents of Little Tall island have Dark Secrets. The Big Bad, being a mind reading demonic sorcerer, lets them know that he knows just to freak them out. He also reveals some of these secrets to the other residents for kicks.
In the Community episode "Mixology Certification" the group learns that Shirley had been hiding the fact she was a barfly during a more troubled time of her life.
In Switched at Birth, Regina knew about the switch and had a private investigator keep tabs on Bay for some time.

Tabletop RPG

GURPS has a Disadvantage called Secret. If it's revealed, the character loses the Secret, but gains Disadvantage(s) (or loses Advantages) worth twice as many points as the Secret.
The Old World of Darkness had a one point flaw called Dark Secret. That it's only worth one point tells a lot about the setting.
The GURPS Disadvantage was inspired by Champions and its system of Disadvantages. The current edition has Social Limitations that include things like Guilty Secret, Dark Secret, Embarrassing Secret, and so on.
Similar to the GURPS example; the BattleTech RPG A Time of War has the negative trait "Dark Secret". These can range from things that could harm the character socially up to something that could trigger an interstellar conflict. Should it be discovered the PC can expect to gain Enemy, negative Repuation and Bloodmarked traits.

Video Games

StarCraft II
- Tychus Findlay. The Dark Secret in question is his deal with Mengsk: he kills Kerrigan, he's free. As he says in the end of the game:

"I've made a Deal with the Devil."

- In the secret mission "Piercing The Shroud", it is discovered that the Dominion is behind the Zerg-Protoss Hybrids, which play a very important part in Zeratul's missions. Yep, that's right: it seems that the Dominion (with some dirty help) wants to bring The End Of The Universe As We Know It.
Ace Attorney has a number of these. Figuring out what they are is the whole point of the game.
Sword of the Stars II: Lords of Winter reveals that the Liir have been harboring a dark secret: the Suul'ka are really Liir Elders who have refused to die and became Drunk with Power. The bit about the Liir killing all Suul'ka with a bio-engineered plague is complete bull.

Web Comics

In Sinfest, when Tangerine tells Seymour to tell the ring his secret, Seymour flashes back to his and reacts strongly.