Arrested Development: At one point the show had Henry Winkler walking along a dock, and had to take a bit of a leap to get past a cartilaginous fish that was lying there.
A Getting Crap Past the Radar example: Lindsay has done a Cheek Copy and shows Michael a picture of that, thinking it's a picture of a car she wants to buy. Michael replies that what she showed him isn't a picture of a Vol-vo (it's a picture of her vulva).
The famous Nantucket limerick shows up in the pilot. Delenn has heard it, and thinks it's a typical example of Earth poetry...
In the B5 prequel, In The Beginning, one of the few Minbari who advocates giving peace a chance is named Lennon. (Word of God confirms that this was intentional.)
There's a customs scene where Zack Allan is explaining customs procedure to a new security recruit. As he mentions that "anything unusual gets flagged", Londo shows up. Shortly followed by Bester. Zack then decides to get out of here before anyone else goes through the customs gate, since for all he knows it could be the Second Coming. After Zack leaves, the next people through the customs gate are...a trio of Elvis Impersonators. According to Word of God:
Black Eyed Peas: Since 2006 Dick Clark's New Year's Rockin' Eve has had the west coast portion that airs after midnight on the east coast hosted by Fergie from this group. In case you do not understand the pun you are traditionally supposed to eat black eyed peas on New Year’s Day to bring you good luck in the upcoming year.
Finally, his band is called "Dingoes Ate My Baby". Dingoes are found in Australia. What's a nickname for Australia? Oz.
In the episode "Tabula Rasa", Spike is being pursued by a demon he owes money to. The demon has the head of a shark. Which makes him... a loan shark.
In another episode, Spike and others are gambling with baby cats instead of poker chips. In card games the betting pool is often referred to as "the kitty".
Burn Notice: In the first season, Michael adopts the persona of good ol' boy Homer to repo a boat. He's working for a man named Virgil.
Cheers: The episode "Little Carla, Happy at Last": Carla finds out she's pregnant by Eddie LeBec. Worse yet, it's twins. She thinks that's bad news but the father disagrees:
Eddie: Twins means we're twice blessed! I can't believe it! This is the happiest night of my life! Sam: You know, I had twins once. It was the happiest night of my life too.
Chuck: Chuck's ability to access data on threats to the country is called "flashing". When he temporarily is unable to do so, he tries to practice, and is shown using a series of cards with images of spies on them, which are never actually called "flash cards".
Until the series' third-to-last episode, "Chuck Vs. The Bullet Train", when the villain Quinn calls the set of special cards he uses to force Sarah's defective Intersect to activate just that.
Also, the title of the fifth season opener ("Chuck Vs. The Zoom", "zoom" being what Morgan chooses to call a "flash" when he's using the Intersect) is a pun on the DC Comics hero The Flash and his number one enemy, Professor Zoom. The pun also foreshadows the deterioration of Chuck and Morgan's relationship over the first third of the season.
The Colbert Report: Has Gorlock, a Signs-esque alien who advises Stephen on various topics. He was first introduced as Stephen's financial advisor and an excuse to make Scientology jokes, but we later find out that he's also Stephen's attorney. Making him... A legal alien.
Was there ever a mention of him taking a sick day? Which would make him an ILL-legal alien.
Cold Case: The episode Beautiful Little Fool opens with the 1929 New Year party in a mansion. In the next scene, one of the attendants is dead. It turns out the killer worked as butler in said mansion, meaning The Butler Did It.
Community: Britta is called a buzzkill by her fellow study group members throughout the series, but it's only in season 5 that she gets to do it (semi-)literally, "killing" Buzz Hickey by pushing him into imaginary lava.
Degrassi: In the franchise, nobody ever called Mr. Raditch "Radish" until JT and Liberty in his actor's last episode on the show.
Dexter: The very name of Dexter Morgan is most likely a Stealth Pun, given that it's Latin for "right." The corresponding term for "left"? Sinister.
Doctor Who: The episode "Aliens of London" features a pig being put into a spaceship and fired at Big Ben in order to create a fake alien invasion which will scare the populace. So the entire plan revolves around a flying pig...
And in "The Parting of the Ways", the Doctor mentions the planet Barcelona:
Doctor: They've got dogs with no noses. Imagine how many times a day you end up telling that joke, and it's still funny!
In "The Curse Of The Black Spot", the Siren disappears injured people away to a hospital sickbay. When someone requires medical attention and help is being sent, it's generally heralded by a siren.
In "The End of Time" the Master turns the entire Human race into copies of himself, and tells the Doctor that the Human race have now become 'The Master Race'. Although this initially seems like an Incredibly Lame Pun, it becomes a Stealth Pun when you realise that The Master has blonde hair and blue eyes.
The story "City of Death" takes place in Paris. Paris is also referred to as "cité de l'amour" (city of love), which is a hononym for "cité de la mort"—city of death.
Farscape: Has Rygel, a deposed king who has a tendency to release farts similar in effect to helium. Should I really point out that helium is a noble gas?
Father Ted: The episode "Chirpy Burpy Cheap Sheep" is about a sheep who is being driven neurotic. There's a concealed pun implicit in this concept (and [formerly] revealed in The Other Wiki'srelevant episode entry) but it is something of a subversion since neither the pun nor the punchline are actually spoken.
Firefly: Overlapping with an ILP, in the episode "Safe", River wanders off and starts dancing — and it's stated in her backstory that she was a ballerina (Real Life Writes the Plot, Summer Glau is one). How is this a pun? Her name is River, and she is dancing. River. Dancing. Riverdance.
In the DVD's scene selection for the episode, this scene is actually called "River Dance."
Frasier: From "Ham Radio", the actor Mel White, whom Frasier even describes as "Man of a Thousand Voices".
Glee: The episode, "Furt", revolves around Finn's mother and Kurt's father marrying, making them into a family. Finn gives a speech in which he says that, as they're together, they should have a portmanteau name (no); they are now "Furt". Left unsaid is that, as of their families joining, they're Kin(n).
Horrible Histories: The Owain Glyndwr song is a pastiche of "Delilah" by Tom Jones - however, when Owain mentions being given the title of Prince... of Wales, it segues into a pastiche of "Kiss", which was also performed by Jones, but originally by Prince.
The Henry VII song (a Glam Rock pastiche): "I said 'This crown ain't big enough for the three of us!' and had one slayed!
How I Met Your Mother: Had an episode where Ted was lecturing his class about the work of an architect who had died midway through his work, leaving it unfinished, and repeating the word "unfinished" until the word lost all meaning. The background music? Schubert's Unfinished Symphony. Might double as a Genius Bonus.
In Last Cigarette Ever, Marshall is shown talking to his 13 year old self, who pulls an I'll Be in My Bunk with a picture of his future wife. That's right, a Picture of Lily
Kitchen Nightmares: In "The Great British Nightmare" special episode, Ramsay's attempts to prove a local restaurant is better than a chain restaurant are accompanied by the instrumental opening of Fleetwood Mac's "The Chain".
LOST: Has a ridiculous amount, if you stop to think about it. Locke — a man known for thinking out of the box — used to work at a box company. Naomi in 4th season didn't have a Ruth, making her ruthless. And in 6th season, episode "The Substitute", Sawyer dangles for a while between the devil and the deep blue sea.
Malcolm in the Middle: One episode has Dewey being menaced by a girl in his class. Reese offers to help him come up with some barbs to throw at her, and suggests finding something that rhymes with her name. Dewey says she's "Regina Tucker", and Reese says that isn't much to work with, but he's sure they'll think of something.
Merlin: This BBC's series features King Uther. He used to keep a dragon penned up in the dungeon.
Mock the Week: Milton Jones comments that farmers have recently started using heroin but finding the evidence has been difficult. It's like finding a needle in a haystack.
Monty Python's Flying Circus: In the fourth-series sketch "A Doctor," a doctor hands a questionnaire to a patient bleeding profusely (where his nurse stabbed him) and gives him failing marks for wrong answers (correct answers include "The Merchant of Venice" and "the Treaty of Versailles"). He never says he's giving his patient an exam.
In the "Killer Joke" sketch, while the British Army conducts testing on the eponymous joke during World War II, a voiceover informs us that it is "50,000 times more powerful than Britain's great pre-war joke" — while the B Roll Rebus briefly shows Neville Chamberlain.
Morecambe and Wise: There was a recurring bit where a former Special Guest would declare "I worked with Morecambe and Wise ... and look what happened to me", before the camera pulled out to reveal they were working in a menial job. Andre Previn turned out to be working on a London bus ... as a conductor.
NTSF:SD:SUV::: In an episode of this [adult swim] show, the villain is a dolphin by the name of Lundgren. Get it...? Dolph Lundgren?
In one episode, Lister suggests a game of squash with Rimmer's light-bee, a device which flies around and projects his holographic image. Squash is a game played with a small hollow ball. Hollow, holo...
The name of Red Dwarf 's subship Blue Midget is based on the main ship's name, with Midget being a synonym for Dwarf, and blue being a different colour.
Revolution: One of the first things Mia talks about is how she was Missing In Action (M.I.A.).
Scrubs: In this episode an imaginary patient has a kitten in his mouth. Probably he misunderstood the concept of eating pussy. Either that or the cat's got his tongue.
Sherlock: Does not once excrete onscreen. Or to put it like a caveman (or somebody with grammar of a similar level) would: no shit Sherlock.
Smallville: One episode is all about nightmares. Every single song in the episode is by REM.
Another has a story where Lionel drove his wife insane - it ends with him listening to Madame Butterfly.
In Escape, Lois was wearing Scottish attire when she was possessed by the (Scottish) Silver Banshee.
The Sopranos: Phil's men are hiding in Vito's motel room, where they ambush and plan to kill him due to the revelation that he's gay. Phil himself is hiding in a closet, and once Vito has been subdued, Phil reveals himself to Vito by coming out of the closet.
Anis: You may call me Anis. It means "Noble Strength". Daniel: I am Daniel. It means "God is my judge". Jack: I'm Jack. It means... what's in the box?
Parodied in that this is an actual conversation change because he didn't know the meaning of his name....
So when it comes to names, he doesn't know Jack.
Star Trek: The Next Generation: A variant appears in the episode "The Naked Now". As the Enterprise crew succumb to an inebriation-inducing virus, Data reports picking up numerous disturbances on internal sensors, including a crewman singing a limerick:
Data: There once was a woman from Venus, whose body was shaped like a— Picard: Security!
And speaking of TNG, there's the emotionless android Data and his more human brother Lore. This borders on Fridge Brilliance.
Top Gear: There is a joke award for the biggest presenter error called the Golden Cock award (a small figurine of a rooster). In the 2009 Top Gear Awards, the award was given to their "tame racing driver," The Stig, who refused to give it back and got quite violent when Richard Hammond tried to take it away from him. So you could say The Stig really likes the cock.
Torchwood: In the episode "Dead Man Walking", after learning how much it sucks to be a zombie, Owen (unsuccessfully) attempts to drown his sorrows in beer.
And then he literally tries to drown himself.
Veronica Mars: The late Lilly Kane called her younger brother Duncan by the nickname "Donut". One (admittedly cute) fanfic posited that it was because he wanted to be a cop as a kid. Someone clearly missed the pun.
In one episode, Veronica hides a listening device in a preserved insect. (It's a bug in a bug.)
Warehouse 13: An artifact-carrying vigilante dresses up as comic book superhero, "The Iron Shadow". According to the comic-loving Lattimer, The Iron Shadow has no powers, he has simply trained himself to near physical perfection. At the end of the episode, briefly-visible text as the artifact is being cataloged reveals it to be Charles Atlas' gym trunks.