Also when Gul Dukat is revealed to be working with the Dominion.
And a few episodes later, when it is revealed that Bashir is in a Dominion prison and has been replaced by a Changeling for most of the season.
Famous early example in Lost is the nature of Locke's "miracle," revealed at the end of episode 4. There are plenty more from the series.
The two biggest reveals come at the third and fifth season finales: what we've thought is a pretty standard despondent-alcoholic-Jack flashback is actually a flashforward, with Jack and Kate off the island and Jack wanting to go back, and the man we've thought is Locke this whole time is actually the series' Big Bad, who has taken the form of John Locke, who was not miraculously brought back to life by the island but has been dead since season three (technically), respectively.
The series finale has the Sideways timeline reveal that their "alternate lives" are actually their afterlife and the entire cast will eventually be Together in Death.
Heroes is not only fond of this trope but loves to do it multiple times on the same subject.
A specific case would be the bomb that will/might/did destroy New York City, which is "revealed" to be caused by one person, then re-revealed to be actually caused by someone else, then...
The episode "Five Years Gone" contains another: President Nathan Petrelli is actually Sylar, using the illusion power he obtained from Candice Wilmer. This is revealed as Sylar is cutting open Claire's skull.
The fact that this actually comes partly true, Sylar replaces Nathan, is more than slightly disturbing.
In the episode "Sleepless", it's revealed that Mulder's new partner Krycek is working for the Cigarette Smoking Man.
CSM is Mulder's biological father. Probably. Ambiguously for several seasons, but somewhat confirmed in the final season.
In the Season 2 (and series) finale of Carnivāle, it's revealed that Sofie is destined to become a sinister figure called "The Omega", and that she possesses supernatural powers very similar to those of her father...Brother Justin Crowe. Earlier than that, there's the revelation that "Management", the mysterious unseen figure that owns the carnival, is actually Lucius Belyakov, the Russian soldier who tried to kill Henry Scudder during World War I. As later learned, he's also the father of Brother Justin (who was born "Alexei Belyakov"), and the previous generation's Avatar of Light]].
There's the very first episode in which Sydney learns that she's actually working for The Alliance, an evil organization that she thought they were fighting, and not the real CIA. Some of the major ones:
Laura Bristow was not a lit professor, but actually a KGB spy by the name of Irina Derevo, and is actually alive and is The Man.
Season Two: Sloane assisted in taking down the Alliance for his own means (arranging for the information that Sydney & co. at Oops Central to be available).
Season Three: Sydney actually erased her own memories of the two years she spent "working" for the Covenant.
Season Four: Jack Bristow actually killed a double of Irina Derevko. The real Irina was being held by her sister Elena in captivity. Elena turned out to be Sofia, the woman running the orphanage that Nadia grew up in.
Season Four/Five: Six words: "My name is not Michael Vaughn." Sloane's flip-flopping between being good and evil does not count because, honestly, who didn't see it coming?
The Dick Van Dyke Show — The Crowning Moment of Funny in "That's My Boy??" is a classic. The episode is a Flashback to when baby Richie came home from the hospital. Over the course of the episode, Rob (Dick Van Dyke) convinces himself that Richie has been Switched at Birth with the baby from the Peters family. He invites Mr. & Mrs. Peters over to reclaim their baby, only to learn when he opens the door that that they are an African-American couple. Rob asks, "Why didn't you—?" and Mr. Peters (Greg Morris) replies, "And miss the look on your face?"
Valyrian steel can withstand the ice weapons of the white walkers.
Bran himself is the source of Hodor's handicap as he accidentally warged into Hodor's past self, causing him brain damage in a Stable Time Loop. Hodor is short for "HOLD THE DOOR!", the final order Hodor received before his death.
Henry is his son and accomplice, making him the killer out of the main group.
Although Henry is just as psychotic as his dad, he has different plans than him; turns out that unlike Wakefield, who simply wanted to wipe out everybody, Henry wanted to kill everybody except for Abbey, and then keep her with him for the rest of their lives to live out his deranged childhood fantasy.
Battlestar Galactica has an on-going mystery about the identity of the twelve Cylon models. The first of many reveals is in the Miniseries, where it is revealed that Sharon must be one of them in the final scene. There are also a few other puzzles:
Season 2: Another Battlestar survived the Cylon Holocaust.
Season 3: Tyrol, Tigh, Tory and Anders are four of the missing five Cylon models.
Season 4.5: The Thirteenth Tribe that colonized Earth were all human Cylon models.
Season 4.5: Ellen Tigh was a Cylon.
Season 4.5: The 'original programmers' were Tyrol, Tigh, Tory, Anders, Ellen and Cavil.
By Season 4, Supernatural seems to be doing an average of one an episode. From off the top of my head, we've had the Reveals that: Dean was rescued from Hell by an angel! Big Bad Lilith plans to raise Lucifer! Dean tortured souls in Hell! By torturing souls, Dean allowed the first seal to be broken, making Lilith's plan possible! Sam can now kill demons with his mind! There are some angels working to help release Lucifer! There are plenty more. To give you some idea, the last 3 reveals were in just one episode.
The Trickster is the archangel Gabriel who, when it comes down to it, is just a bitter, jaded kid who didn't want to see him family fight.
Lilith was not working to break the final seal, she WAS the final seal, and Ruby was manipulating Sam to get him to kill her. "The first demon shall be the final seal."
The colt doesn't work on Lucifer.
Season 6: Sam is soulless! The Campbells are working for Crowley! And up to eleven in the last 4 episodes of that season: Crowley isn't dead! Castiel is working with Crowley to open Purgatory! Cas raised Sam from the pit! Cas is the Big Bad!
In "Utopia", there's the revelation that Professor Yana is The Master (who survived the Time War and hid as a human with a Chameleon Arch), and the Face of Boe's message was a secret acronym hinting at this (You Are Not Alone). Then, when The Master is shot and regenerates, it's revealed that Prime Minister Harold Saxon (an unseen figure frequently alluded to in Season 3) has been The Master all along.
"It's us!", if you hadn't guessed it an episode earlier.
Who is the Pandorica's intended occupant, the "nameless, terrible thing, soaked in the blood of a billion galaxies", the "most feared being in all the cosmos"? It's the Doctor. His enemies constructed the Pandorica to trap him.
River Song's true identity. She's really Melody Pond, Amy and Rory's daughter from the future. And she's the one destined to kill The Doctor, at the behest of the Silence.
Technically, Jack's immortality, though it was revealed in episode 1 of Torchwood.
Jack being the Face of Boe.
The truth behind the multiple incarnations of Clara Oswin. The one from the 21st century is the "real" one; the others exist because Clara was forced to enter the Doctor's timeline to stop the Great Intelligence from changing it, creating duplicate versions of herself without her memories.
The War Doctor actually ended the Time War by trapping Gallifrey in a pocket dimension to save it from the Daleks' onslaught. The Doctor's home planet is still out there!
Missy finally reveals her true identity: The Master regenerated as a woman.
"The Zygon Invasion"/"The Zygon Inversion" two-parter introduces the mysterious "Osgood Box" as a Macguffin that can supposedly lead the Zygons to victory against Earth, and promises that the Zygons will learn why it's called an "Osgood Box" as soon as they find it. When they do, it turns out that it's because there are two boxes, just like there are two Osgoods. One of the boxes will kill every Zygon on Earth if it's triggered, and one will cause the Zygons to revert to their natural forms; no one knows which is which, just like no one knows which Osgood is human.
When Dr. Brennan finds out that her parents were actually notorious bank robbers.
Used when the team discovers that Zack is Gormogon's apprentice.
In the Season 3 ER episode "Night Shift," a patient who is badly mangled after jumping (or falling) onto the tracks in front of an elevated train is rolled into a trauma room. Dr. Benton tells a nurse to page Benton's favorite medical student Dennis Gant, and everyone is horrified when the patient's beeper goes off—it's Gant on the table!
Rudy Cooper, a guy working in the hospital who is dating Debra, is The Ice Truck Killer; the Serial Killer who the PD hunt and who plays friendly games with Dexter.
The Ice Truck Killer is Dexter's biological brother.
From the third season premiere: Rita is pregnant.
From the 4th season finale: Rita was the Trinity killer's last victim.
Late 6th season: Professor Gellar is shown to have been dead for some time and only alive in Travis' imagination.
In the Season 8 episode of Stargate SG-1 "Prometheus Unbound," Daniel is the only person left aboard the Prometheus with one of Anubis's Super Soldiers. After Daniel is captured and tied to a chair, the Super Soldier hits on Daniel, who is understandably disturbed. Then the Super Soldier removes its helmet to reveal Vala Maldoran.
Jack & Bobby pulled this off in the pilot episode, waiting until the very end to reveal which of the show's two brothers would grow up to become President.
Season 1: The Flash's mentor, Professor Wells, is an imposter and a time traveller called Eobard Thawne who is just using the Flash to travel back into the future.
Season 2: 'Jay Garrick' is a timeline remnant, of speed-devouring villain known as Zoom whose spying on them and his real name is Hunter Zolomon.
Season 3: The crime scene investigator Julian Albert is chosen by the so-called god of speed, Savitar as his chief disciple.
Savitar is later revealed to be a future incarnation of Barry Allen.
In season 4 of NCIS, Tony's relationship with Dr. Jeanne Benoit was allowed to progress for many weeks, and to get quite serious for both of them, before it was revealed that he'd engineered the relationship to investigate her arms-dealer father, and hadn't even told her his real name.
JAG: In "Boot", Private Schuler's killer was Private Whitley, who appeared to be the nicest character in the episode.
Noah's Arc has plenty, but a major one that stands out is Junito's HIV status.
Season 8 concludes with, at long last, the Mother's first appearance (though, with all the clever twists and turns that happen on this show, we're never quite sure of anything).
So far, Season 9 is just Reveal after Reveal about how Ted's relationship with the Mother will go.
Many episodes in the second season of Breaking Bad begin with enigmatic Call Forwards showing heaps of debris being pulled out of Walt's pool by men in Hazmat suits, including many repeated close-ups of a battered pink teddy bear. Taken out of context, they make no sense. Then in the Season 2 finale, it's revealed that the debris is actually from a plane collision over Albuquerque that Walt inadvertently caused when he allowed Jane Margolis to die of a heroin overdose, thus leaving her father David (an air traffic controller in his day job) so distracted by grief that he let two planes collide in mid-air. Out of context the scenes were probably meant to trick the audience into thinking that Walt relocated his meth lab to his house, and then it exploded catastrophically, possibly killing him or his family.
Given that the premise of Ashes to Ashes is that the main character - Alex - has no idea where she is, the show has many big reveals which change the course of Alex's investigation.
Gene Hunt is present in Alex's memories, implying that she has experienced time travel and is not in a coma.
Martin Summers is sharing this world with Alex, which implies that the world is infact real and not a hallucination.
The world is finally revealed to be a Purgatory for dead coppers, and Gene Hunt has known all along. Chris, Ray and Shaz are also real but have forgotten about their previous lives.
René Lenier is actually Drew Marshall, a man who killed his fangbanger sister and then fled his hometown, and was the perpetrator of all the murders during season 1.
Maryann is a Physical God hellbent on sacrifice. Tara accidentally summoned her in season 1.
Bill was working for Sophie-Anne, having been specifically sent to procure Sookie. He then constructed a gambit in which two psycho's beat Sookie within an inch of her life so he could feed her his blood and build a connection with her.
Russell Edgington murdered Eric's family.
It was Marnie who was controlling Antonia, not the other way around.
The very last scene of season four of The Good Wife: It's Carey at the door, not Will.
24 pulls these on a regular basis, generally to show which side a character is now on or reveal their true motives. There's too many to list, but the most famous ones are the reveals of Nina Meyers and Charles Logan as villains. Occasionally a character the protagonists were attempting to save is discovered to already be long dead (namely Teri Bauer in season 1 and Omar Hassan in season 8).
So far, every episode of Sherlock has had one of some kind.
"A Study in Pink": The killer is the taxicab driver, and he got the victims to commit suicide by forcing them to choose between two pills at gunpoint (one harmless, one poison).
"The Blind Banker": The spray-painted symbols are ancient Chinese numeric symbols—each referring to a page in a London street atlas that leads to the smugglers' hideout.
"A Scandal in Belgravia": Irene's cellphone contains evidence of a secret Ministry of Defence ploy to save a group of plane passengers from a terrorist attack. Mycroft wants to replace the passengers with stolen corpses so that the terrorists don't realize that Military Intelligence has cracked their codes.
"The Hounds of Baskerville": The "monster dog" that killed Henry's father was really Dr. Frankland, seen through the eyes of a hallucinating Henry. Frankland and Henry's father previously developed a hallucinogenic chemical agent while working together on a CIA project called "H.O.U.N.D."; the chemical caused Henry to see Frankland as a monstrous dog because he was wearing a sweatshirt with "H.O.U.N.D." written on it.
"The Reichenbach Fall": Moriarty has been living a double life as a television actor named "Richard Brook". His ultimate plan is to discredit Sherlock by convincing the world that he staged the two's rivalry as part of a publicity stunt.
"The Empty Hearse": Lord Moran arranged his "disappearance" by detaching a subway car in the London Underground and using it to hide his explosives. Also, Sherlock faked his death by falling on a hidden inflatable mattress, temporarily stopping his pulse with a squash ball, and paying members of his homeless network to pose as paramedics.
"The Sign of Three": The Mayfly Man was plotting to kill Major Sholto all along, and he infiltrated John's wedding by posing as the wedding photographer. He kills his victims by stabbing them with a blade so fine that they don't feel it, and positioning the stab wound so that the victim's belt puts enough pressure on the wound to hold it closed—allowing him to escape before his victims realize that they've been killed.
"His Last Vow": There's no vault in Appledore. Magnussen stores his blackmail information in his mind, because he's able to use the same "mind palace" technique that Sherlock uses. Mary is actually a former assassin. Moriarty is possiblyNot Quite Dead.
"The Abominable Bride": With the case itself, Emilia Ricoletti faked her suicide long enough to kill her husband before killing herself for real. She and her friends were members of a women's rights group that were murdering the men who abused them. More broadly, the episode is not actually an AU-version of the normal show, but is connected to the main plot; it's Sherlock's drug-overdose-induced hallucination to try to solve and cope with the reappearance of Moriarty. Sherlock also concludes that Moriarty really is dead, and his "reappearance" is someone else impersonating him.
"The Six Thatchers": "AGRA" is not actually Mary's real initials, but the initials of the first names of the four members of the assassination/black ops group that she was a part of. "AMMO", the mystery person on the phone who sold them out, is not actually Lady Smallwood, but her secretary, Vivian Norbury.
"The Lying Detective": Philanthropist and public icon Culverton Smith really is the serial killer Sherlock accused him of being. The woman who visited Sherlock at his flat claiming to be Culverton's daughter Faith really was there (and not a drug hallucination as Sherlock feared), and she, John's new therapist, and the woman John flirted with on the bus in the previous episode are all the same person: Sherlock's and Mycroft's sister Eurus Holmes.
"The Final Problem": Redbeard was not actually Sherlock's dog. It was his (human) best friend that he used to play pirates with (and the boy's pirate name was "Redbeard"), and Eurus killed him out of jealousy because she wanted to play too.
Boardwalk Empire: In Season Four's second-to-last episode, Roy Phillips, who has presented himself to Gillian as an innocuous businessman and has been romancing her all season, reveals himself to be a Pinkerton agent who's really there to investigate the death of Roger, the Jimmy lookalike whom Gillian murdered so she could have Jimmy declared legally dead. His Batman Gambit (apparently shooting and killing someone who lost his job because of Roy) was a ruse to get Gillian to confess to murder.
American Horror Story: Asylum opens with Kit Walker accused of being the Serial Killer "Bloody Face", and promises a big reveal about the truth behind Bloody Face's identity. As revealed in "I Am Anne Frank", it's Dr. Thredson. Grows another layer in "Coat Hanger", when we learn the connection between the present-day Framing Device and the 1960's scenes; turns out that the second Bloody Face is Thredson's son Johnny, and Lana is his mother.
Howdy Doody combined this trope with a massive Tearjerker. Throughout the entire series, Clarabell Clown never spoke a single word, using his face and a horn to communicate with other characters. The last episode, aptly titled "Clarabell's Big Surprise," promised that the clown would reveal something huge to viewers. After dropping hints throughout the episode, the "big surprise" was revealed—Clarabell was able to talk! Buffalo Bob urged him to prove his secret, as it was his first and last chance. A drum roll played as the camera zoomed in on Clarabell...and he softly whispered "Goodbye, kids." This was the final moment of the program.
Kirsten's roommate Camille is secretly a member of the Stitchers program.
Billions offers a twofer reveal in its debut episode: the wife of US Attorney Chuck Rhoades is not only the house therapist for hedge fund manager Bobby Axelrod, whom Rhoades is investigating for insider trading, but also the dominatrix torturing Rhoades in the very first scene!
Mombi had been using magic to disguise Tip as a boy since infancy.
"Lions in Winter" shows that not only is Eamonn the show's version of the Cowardly Lion, as revealed by his armor that's adorned with a lion's head, but he's also the one who murdered King and Queen Pastoria.