In V for Vendetta, V confronts Lewis Prothero with a recreation of the Larkhill Death Camp that he once ran, which resembles the minimal set against black drapes used by Number Two to recreate Number Six's childhood in "Once Upon a Time".
In The League of Extraordinary Gentlemen: Black Dossier, the Village is referenced as an installation of the Thought Police during the Big Brother regime, the government having put out a contract for "dream inducers and killer balloons for some Welsh set-up", alluding to the seriess real-life location.
In Crisis on Infinite Earths, Batman threatens the Joker with a reference to the show: "The only movie you'll be starring in is a remake of The Prisoner — and I don't mean the one in that village!"
One issue of Miracleman: The Golden Age is set in a nameless "City", which turns out to be where all the world's spies were sent because they were too paranoid and amoral to live in a Utopia (they all believe that most of the other people are the innocent civilians they're protecting). At the end of the story it's revealed that the City is run by the resurrected Evelyn Cream, who introduces himself as "Number One". He chuckles after saying this, suggesting that it might in-universe be a deliberate joke referring to the show.
In the story "Zero Zone" in issues 106-107 of Sonic the Comic, Sonic is taken to a zone resembling the Village and brainwashed into believing he is 'Citizen Seven'. The zone features a pink bouncing ball that immobilises and incapacitates Sonic when he tries to escape. It is revealed at the end of the story that the zone's ruler, 'Citizen One', was actually a computer program designed by Dr. Robotnik who broke free of its programming and created the fake reality due to loneliness.
The Invisibles contains several references to the series. In the collection Entropy in the UK, King Mob is captured by government agent Sir Miles Delacourt; they exchange the show's famous opening lines: "What do you want?" "Information." "You won't get it." "By hook or by crook, we will." A major character in the series is referred to as "Mr. 6".
In The Matrix, as Neo is running from Agent Smith in an apartment building, we see an elderly lady in one of the rooms; while Agent Smith transports inside her and launches a knife at Neo we see that she was watching an episode from the series.
In Twin Peaks: Fire Walk with Me, Mrs Tremond's grandson covers his face with a mask and then removes it to reveal the face of a monkey in much the same way as Number Six removes Number One's masks in "Fall Out".
In the Doctor Who New Adventures book Human Nature (though not the TV episode adapted from it) the little girl's balloon can, like Rover, hunt down and kill people.
Live Action TV
A 1969 episode of The Avengers, "Wish You Were Here", is influenced by The Prisoner, as Tara goes to visit her uncle and finds him held in a hotel with every attempt at escape thwarted by 'accidents'.
In Babylon 5, the Village's "Be seeing you" greeting is used in modified form as a recognition symbol for a fascistic telepath-supremacist movement. In fact, McGoohan was supposed to guest star as Knight Two in "And the Sky, Full of Stars", but was unavailable.
In "The Sea Devils", the Master is imprisoned by the British government, guarded by men who all wear cloaks and badges, and drive about in quirky white cars.
The episode "Heaven Sent" has the Doctor trapped within a castle within which an unidentified entity uses various methods in order to try and extract secret information from the Doctor.
In the Hercules: The Legendary Journeys episode, "Stranger in a Strange World", Iolaus is locked in a prison cell and is told he will only be released when his numeral is called. Iolaus then exclaims, "I am not a numeral! I am a free man!"
J. J. Abrams has said that "I loved The Prisoner, which was a very odd sort of hybrid of sci-fi, mystery and character, and certainly there are elements of The Prisoner in both Alias and Lost". The iconic bicycle logo is featured in an episode of Fringe where a special agent's memories are reprogrammed. In a later Fringe episode, "Letters of Transit", the character of Walter Bishop calls out "I am not a number, I am a free man" while in a delusional state.
The British sitcom 2point4 Children features a lengthy tribute to the series in the episode "Seven Dials", where one of the central characters is imprisoned in Portmeirion by an opponent.
Wayward Pines is blatantly inspired by The Prisoner, but the most overt reference happens when Theresa is ordered to work for the estate agent "Big Bill", and he greets her by saying that she is his "new Number Two".
Iron Maiden did a song called "The Prisoner" their album The Number of the Beast. Inspired by the series, it features dialogue from the title sequence: the band's manager, Rod Smallwood, had to contact Patrick McGoohan to ask permission to use it for the song. According to witnesses, the usually calm Smallwood was completely star-struck during the conversation. McGoohan was reported to have said, "What did you say the name was? Iron Maiden? Do it." The band later recorded the song "Back in the Village", on the album Powerslave, which contained lyrics referencing the series, such as "I'm back in the village", "I see sixes all the way", "Questions are a burden, and answers a prison for oneself" (quoting a sign seen in "Arrival)" or the final line, "I don't have a number, I'm a name", a tweaked version of the catchphrase "I am not a number, I am a free man". Bruce Dickinson's second solo album 1994's Balls to Picasso features the dedications "Inspired by number 6" & "Be Seeing you" within the cover. Dickinson's song Broken from his The Best of Bruce Dickinson compilation features the "I will not be pushed, filed, stamped" quote within the lyrics.
The official promo for "Alright" by Supergrass is filmed in Portmeirion and features many iconic images from the series.
Rover shows up in the 550- and 580-point versions of Colossal Cave, if the player uses the wrong password to enter the vault.
In Citadel for the BBC Micro, the player cannot leave the area called "The Island" to the right — the last screen has a multicoloured globe that acts like Rover and blocks their progress.
Batman asks Talia whose side she is on. "That would be telling," she replies.
Batman has an exchange with some thug called "Twitch".
Twitch: What do you want? Batman: Information...
During the Pinky and the Brain episode "Brainwashed", there is a segment in which the main characters are sent to a village where the residents are only identified by the hats they wear, in addition to other homages to the original series.
ReBoot episode "Number 7" makes a number of references to the series, including visual references such as Number 2's oval chair, quotes such as "I will not be pushed, filed, stamped, indexed, briefed, debriefed or numbered!" and a scene that recreates part of "Fall Out".
In Shrek, the entrance of Shrek and Donkey at the seemingly deserted village of Duloc echoes Number 6's Arrival in the Village. The font on the village's signs in Shrek is the same as in the Village, and the architecture of the buildings is similar as well.
The third chapter of The Simpsons episode "The Computer Wore Menace Shoes" is basically a seven-minute reference to this series, complete with McGoohan reprising his role as Number Six. The scene in "The Joy of Sect" where Marge escapes the Movementarian camp is also a reference to this series. Furhermore, the close up shot of Krusty's face behind bars in the beginning of act two of "Krusty Gets Busted" is a reference of the closing credit motif of the series.
In SpongeBob SquarePants, episode 130, Mr. Krabs says "Questions are a danger to you and a burden to others." This is a reference to the phrase "Questions are a burden to others; answers a prison for oneself seen on a sign in the Labour Exchange in "Arrival".