Red Dwarf. Hawking appeared in a special programme about the popular British science fiction series. He praised its creators for their witty use of (pseudo) scientific theories and said he enjoyed watching the show.
At the beginning of the Season 6 cliffhanger, "Descent, Part 1", Data is seen playing poker with holographic depictions of Stephen Hawking, Sir Isaac Newton, and Albert Einstein. Hawking portrayed his own hologram for this episode, making him the only guest in any Star Trek series to play himself. When taking a tour of the set, he paused at the Warp core, smiled, and said, "I'm working on that." During the tour, Hawking requested, and was allowed, to sit in the captain's chair of the Enterprise-D.
Stargate Atlantis. In the 5th season of Stargate Atlantis, episode 16 "Brain Storm", where many world physicists were invited to a demonstration of cooling effect using a wormhole between 2 universes. Stephen Hawking, played by an actor, was shown in his chair from behind.
The Theory of Everything. Portrayed by actor Eddie Redmayne in a biopic about Hawking from the early 1960s to the 1980s. Hawking agreed to allow the filmmakers use of his speech synthesizer voice for the film.
Futurama. Hawking has made several guest appearances in Futurama.
In "Anthology of Interest I" Hawking appears as a member of the Vice Presidential Action Rangers, who guard the space-time continuum. Along with Hawking at the end of the twentieth century they include Al Gore, Nichelle Nichols, Gary Gygax, and their summer intern Deep Blue. He first appears as a customer at the pizzeria where Fry mistakenly believes him to have invented gravity for which Hawking accepts credit ("Yeah, sure. Why not?"). After learning of Fry's inter-dimensional experience, he arranges for him to be kidnapped by the VPAR.
In the film The Beast with a Billion Backs, Hawking appears as his own head in a jar leading a scientific convention organized to study and discuss a tear in the universe. He says that despite writing a book about it, he has no idea what it is. After stunning Professor Farnsworth and Professor Wernstrom with beams from his eyes, he is surprised, remarking, "I didn't know I could do that". Hawking provided his "own" voice for this appearance, and is characterised the same way as in The Simpsons.
The Simpsons. Made several guest appearances on the long-running prime-time cartoon:
In "They Saved Lisa's Brain", Hawking saves Lisa from the power-hungry Springfield chapter of Mensa in a special wheelchair, complete with an Inspector Gadget–style retractable helicopter attachment and a spring-loaded boxing glove. In the episode, Homer says to Lisa "Did you have fun with your robot buddy?". Earlier, Homer mistakenly calls Hawking Larry Flynt.
During the British Comedy Awards 2004, Hawking was presented with a one-off toy version of himself in Simpson form by Matt Groening, complete with boxing glove. Hawking presented Groening with a lifetime achievement award.
In the Season 16 episode "Don't Fear the Roofer", he is a friend of Lenny and the owner of the Little Caesars restaurant down the block from Moe's Tavern. Prof. Hawking shows up to explain that Bart could not see Homer's new friend Ray (guest voice Ray Romano) during one scene because there was a black hole between Homer and Bart, thus drawing away the light coming from Ray to render him essentially invisible to Bart, thus enabling Homer to prove his sanity after being institutionalized.
In the Season 18 episode "Stop or My Dog Will Shoot", Santa's Little Helper encounters Hawking in a corn maze while searching for a lost Homer. Hawking says "This maze is too hard for me," and then flies off in the helicopter attachment.
The Wrong Coast. A segment of the show tells about a movie called Party Time Continuum, in which Hawking is portrayed as a time-travelling party-animal played by Seth Green.
Weebl and Bob. In their clip Balance, Stephen Hawking flies across the screen in his buggy and the various characters play around with his speech synthesiser against his will, making it say strange things, such as "I've wet my pants".
Knocked Up. Jonah, while playing in a wheelchair, does an imitation of Hawking by saying (in a robot voice) "People think I'm smart because I speak in a robot voice."
The Vicar of Dibley. In the episode 'Winter' from the Seasonal Specials, when casting for the Christmas Nativity play, Frank Pickle decided to base his version of the Wise Man on Stephen Hawking, speaking in a voice that sounded only slightly similar to Hawking's synthesized voice.
Father Ted. In the episode 'Are you right there Father Ted' from the Third Season, Father Dougal mentions an occasion when Father Ted had done an impression of Stephen Hawking in a variety show only for Stephen Hawking to turn up unexpectedly.
Whose Line Is It Anyway?. During a game of "Scenes From a Hat", one of the suggestion that got pulled out was "Celebrities who shouldn't release rap records". Brad Sherwood made a reference to Stephen Hawking who "shouldn't put out a rap record".
Seinfeld. In the season 4 episode The Handicap Spot, when Kramer and George are shopping for a wheelchair for a handicap woman, the store owner introduces them to the brand new, expensive "Cougar 9000" and that he put Stephen Hawking in one of them and "he's loving it!". In the season 9 episode The Butter Shave, Jerry calls George "Stephen Hawking" when he sees George in a power chair, recently given to him by his boss, believing that George has injured both legs. George's boss later finds out George's legs are okay when he sees George trying to flee from a group of old people chasing him on power chairs. He is running on both legs, and carrying the power chair (after it lost power) as a way to escape the old people faster.
Malcolm in the Middle. In one episode, the title character's friend, Stevie Kenarban, was so sad that his mother left his father, he talked by using a machine similar to that of Stephen Hawking.
The Big Bang Theory. In the pilot episode Howard Wolowitz brings over a tape, stating that it is a Stephen Hawking lecture recorded in 1974, "before he became a creepy computer voice." In an episode in Season 2, Leonard impersonates a fellow physicist's impersonation of Hawking on the phone. In an episode in Season Four, it was mentioned that Sheldon had been tricked by his friends into going to the airport at 2AM to meet him. In Season 6 episode 6, Sheldon Cooper and Stephen Hawking also engage in a game of 'Words with friends' over internet. The two come up with pet names of Coop and Rolling Thunder. In the end, to Sheldon's dismay, Hawking insults him.
The Double. Oliver explains a null hypothesis. The null hypothesis Oliver uses is 'Stephen Hawking is not Cassius.' He then states, look through the pictures and show that Rolling Thunder is not Cassius.
The IT Crowd. In episode 4 of season 3, "The speech", Roy and Moss present "The Internet" to Jen, under the form of a small black box, explaining that she can touch it as "it has been demagnetized by Stephen Hawking himself."
The Colbert Report. Stephen Colbert, in character as a right-wing conservative pundit ala Bill O'Reilly, has frequently featured segments entitled "Stephen Hawking is Such an A-Hole", citing reasons such as the 'megalomaniacal' title of his program, "Stephen Hawking: Master of the Universe". "There is only one master of the universe," Colbert responded, "and that's He-Man."
Goodnight Sweetheart. Stephen Hawking is referred to by time-traveller Gary Sparrow twice: in an early episode Gary tells his friend Ron that "apparently Stephen Hawking thinks that time travel could be possible due to black holes" and continues "That's the easy bit. Now tell me why time travel gives me wind."; and in a later episode Mine's A Double when trying to solve the problem of Gary being split into three personalities in clones of his body – when Ron questions his observations of the disruption of the space-time continuum, Gary remarks "Well unless anyone's got Stephen Hawking's phone number I suggest we give it a try".
Sliders. In season 1 episode 7 "Eggheads", Quinn Mallory, in order to understand the rules of the MindGame (a game for which his alternate himself is a superstar in this Universe where mind prevails over physical abilities), read a book entitled "MINDGAME Rule Book - How to play How to win" written by Stephen Hawking.
The Avengers (2012 film). When Captain America and Phil Coulson are on the Quinjet talking about Bruce Banner, Phil mentions Stephen Hawking, but Captain America does not know who that is.
The Critic. Jay and his new trucker friends go to see "Ultimate Force" at a drive-in, which one of the truckers states will most definitely feature "a tough guy on wheels." The movie turns out to feature Hawking discussing his theories on relative force.
Dilbert. Was portrayed in an episode about Dilbert's project, the Gruntmaster 6000, whose "graviton generator" could create a black hole to wipe out all life on Earth. In "field testing" done without consulting Dilbert, the Gruntmaster 6000 was sent to a family in Squiddler's Patch, Texas, where a family of four, living in a trailer, and rather stupid, somehow destroyed the graviton generator, and created a black hole. During the episode, it is "revealed" that Hawking has the power to travel through both time and space via wormholes, and Dilbert learns the hard way that you should never bet money that a theoretical physicist can't do something. Hawking in this also calls Dilbert a "cheap bastard" for only borrowing his book in a library.
The Fairly OddParents. Hawking appeared throughout the episode "Remy Rides Again", in a mechanical flying wheelchair with a rocket on the back of it, which at the end of the episode, disappeared in a way similar to that in which the DeLorean went back in time in Back to the Future. Hawking was played by Dee Bradley Baker in this episode. Hawking was hired by Remy to prove that 2+2=5, and was also Crocker's room-mate in college. Then Crocker found out that 2+2 actually equaled 6, at which he runs after Hawking to brag.
Hawking's persona was first featured in the episode "Peter, Peter, Caviar Eater"; it is a very brief cameo during the song "This House Is Freaking Sweet"; Hawking is presented as the man who will help Chris do his homework. During this time he is tapping his foot.
A character known as "Disabled Guy" or "Quadriplegic Guy" appears to be largely based on Hawking. The character made his first appearance in the episode "Ready, Willing, and Disabled", as a competitor in the Special People's Games. He appeared a second time in "Brian the Bachelor" as an applicant for a reality TV show known as The Bachelorette.
Stephen Hawking talks to reporter Tricia Takanawa in the eighth season episode, "April in Quahog", about the first directly observable instance of a black hole. Hawking tells Takanawa, using his electronic voice, that the discovery "validates the work of a lifetime" before getting out of his wheelchair and talking in a "regular" voice. He is then thrown a surfboard which he catches and with which walks off, telling Takanawa, "see ya, bitch" ("see ya, ching chong" on the DVD release).
In the episode The Old Man and the Big 'C', Hawking is seen streaking at a baseball game, saying "Haha, you are all looking at my penis, you didn't plan on it, but it's happening".
FoxTrot. Jason, designing a computer game called .0005 Life on his computer, comments to Peter about the game's advanced AI ("The guys you'll be fighting won't just be smart, they'll be SUPER smart!). Seconds later, he demonstrates this to Peter by having Hawking attack the character he is playing the game as, adding that "[Hawking's] wheelchair shoots missiles."
Jimmy Neutron. Jimmy, Sheen, and Carl are in the lab, and Sheen asks what guy Jimmy is going to be for Halloween. Carl goes through a series of famous scientists, the last one being "That smart guy in a wheelchair."
Pinky and the Brain. In an episode in which a black hole is used as a weapon, Pinky throws it out of a hotel room window in defiance of the laws of physics. Brain notes that he must consult with Stephen Hawking.
Hawking is seen in a line of people about to board a space ship to Mars in "Life's A Glitch, Then You Die", a segment of "Treehouse of Horror X", in which the Earth is doomed by the millennium bug.
Hawking is also referenced in the episode "The Great Louse Detective" where Sideshow Bob is temporarily released to help Homer find a person who is trying to kill him. Homer lists Stephen Hawking as someone who would want to kill him.
MC Hawking. The imaginary alter-ego for the "theoretical physicist turned gangster-rapper", MC Hawking's songs parody Hawking's distinctive speech synthesiser. Song titles include "E=MC Hawking" ("I explode like a bomb/no one is spared/my power is my mass times the speed of light squared"), "Fuck the Creationists" ("Fuck the damn creationists I say it with authority/because kicking their punk asses be my paramount priority") and "Entropy" ("You down with entropy?") The success of the MC Hawking amongst internet users eventually led to a 'greatest hits' compilation CD entitled A Brief History of Rhyme (a play on Hawking's A Brief History of Time book title), featuring album artwork done by comic artist Tony Moore. Hawking himself is reported to have said that he is "flattered, as it's a modern day equivalent to Spitting Image".
Robin Williams, on his 2002 DVD Robin Williams: Live on Broadway, mentioned that "I called Stephen Hawking's house once", and proceeded in a mechanical voice: "Hello this is Stephen Hawking." "Yes, I'd like to leave a message." "No. This is Stephen Hawking.". On the B-side track 'Boston' of the CD release of the 2002 comedy tour, Williams mentions that "MIT is the only place Stephen Hawking can do comedy" followed by a René Descartes joke.
The Voyage. The New York City Metropolitan Opera commissioned an opera in 1992 by composer Philip Glass to commemorate the 500th anniversary of Columbus's arrival in the New World, which featured a wheelchair-using scientist based on Stephen Hawking. Glass also wrote the music for the documentary A Brief History of Time.
Turbonegro. Hawking's voice is featured on the song "Intro: The Party Zone" on Turbonegro's 2005 album Party Animals, saying "Greetings. My name is Stephen Hawking. Anyways... Please follow our denim leaders as they enter the final black hole; a new dimension in rock music. Welcome to the Party Zone."
Lemon Demon. Lead singer Neil Cicierega sings "I'm on fire, I'm on a big train; going faster than Stephen Hawking's brain" in their song "Boat," from the album "Live From the Haunted Candle Shop."
YES. The band used the lyrics "Hawking's Mind" in the song "Real Love," featured in their 1994 album, "TALK."
Bloodhound Gang. In the song "Boom", Jimmy Pop mentioned "I squeak like Stephen Hawking, Yeah, But I'm Walking."
Symphony of Science. In the original production by John Boswell, portions of Hawking's Universe series were used as lyrics and included in 'A Glorious Dawn'.
Radiohead. Stephen Hawking is often mistakenly thought to have given his voice to "Fitter Happier" on Radiohead's album "OK Computer". It is actually singer Thom Yorke's computerised voice.
Nice Peter. Stephen Hawking, played by Nice Peter himself, appeared in the seventh "Epic Rap Battle[s] of History" against Albert Einstein. It was not revealed who was claimed victorious, although, according to the YouTube community, Hawking came out victorious.
The FuMP. In Volume 1, the song "Talk Nerdy To Me" (a spoof of "Talk Dirty To Me") includes a Stephen Hawking-like voice near the end of the song, which is an acknowledgement of Hawking's references with "nerd" culture.
The Coming of the Quantum Cats. Several Hawkings from different alternate universes ("in varying states of health") make a cameo appearance in this science fiction novel by Frederik Pohl. They are all involved with their particular Earth's plans to develop technology that would allow travel between alternate universes.
Dominic Deegan: Oracle for Hire. Recently, the title character became a teacher at the famous School of Arcane Arts, where he teaches a class called "Secrets of Divination". At the end of his first class, he conjures up a rather large book entitled A Brief History of Everything (Unabridged Version) by Steven Hawkman, the required reading for his course. The name is a paper-thin allusion to Hawking himself, while the title is a slight alteration of A Brief History of Time. 
Hyperion Cantos. Hawking's name appears across the tetralogy under the terms such as the Hawking drive and the name of the Hegemony frigate HSS Stephen Hawking.
Extremely Loud and Incredibly Close. The main character, nine-year-old Oskar Schell, writes letters to Stephen Hawking frequently and once even receives a letter by Hawking that is addressed directly to him.
The Onion. Satirical newspaper ran an article claiming that Hawking had constructed himself a super-powered robotic exoskeleton, complete with a jetpack and claws that can rip through tanks. Hawking, with his typical good humour, sent them a letter cursing them for exposing his evil plans for world domination. Hawking also had a printout of the article pinned up in his Cambridge office for some time after it was published.
Ultimate X-Men. In Ultimate X-Men #25, there is a reference to Stephen Hawking having written an article on mutants, apparently stating that they were mankind's last hope against the rise of artificial intelligence. This makes him one of the rare humans who sympathize with mutants. In addition, the Earth 616 continuity has stated or hinted more than once that Hawking and Hank McCoy (the Beast) are close friends.
JLA. Batman manages to defeat the supervillain Prometheus by replacing the martial arts skills Prometheus had downloaded into his mind with the physical skills and coordination of Hawking. Batman later commented that this was the "first time [he] ever hit a man with motor neuron disease".
Atomic Robo. Hawking creates a fake psychological profile of ATOMIC ROBO indicating the robot hero has a power-standby mode, thus making him an ideal candidate for an envoy for the Viking mars lander. As ATOMIC ROBO does not have a power-standby mode, this leads ROBO to spend the entire Ten month trip without sufficient means to stave off boredom/maintain sanity.
Hyperion. In this novel by Dan Simmons space travel ships are driven by "Hawking drive". This drive was invented by 'race' of Artificial Intelligences (AIs), and allows to make faster-than-light flights.
The DVD release of "Harry Potter and the Prisoner of Azkaban" has a picture of one of the wizards in the Leaky Cauldron reading "A Brief History of Time" while using magic to stir his coffee.
British Telecom (BT). Hawking appeared in and did the voice-over for a BT television advert which aired in 1993. Parts of his voice from this were sampled by Pink Floyd and used on their album, The Division Bell which was released in 1994.
Chapman Brothers. The British artists produced a sculpture entitled Übermensch depicting Hawking in his wheelchair on top of a rocky outcrop.
Go Compare. Hawking announces at a press conference he has formulated the properties needed to generate a black hole; a press reporter asks what Hawking plans to do with it, which leads to a cutaway of the black hole being used to suck in Gio Compario.
Hello Kitty: Happy Party Pals. In this video game, the character Jody often talks about Stephen Hawking, and loves to read his books. Also, an obtainable item in the game is a Science Book, whose description reads: "A Brief History of Time, by Stephen Hawking"
Phil Hansen. In Phil Hansen's breakout art piece Influential, Stephen Hawking was referenced in 5 of the layers of influence, with one clearly being of Hawking himself. "He affected my outlook on life. He made me think about what life is and what I should do with it."
Mass Effect. In the video game series, there is a nebula called "Hawking Eta", most likely named after Stephen Hawking. In Mass Effect 3 one of the characters mentions that they served as a fighter pilot aboard a carrier called the "SSV Hawking". Human carriers in the game's universe are named after great leaders, artists, and intellectuals. This ship is named in honour of Stephen Hawking.
Microshaft Winblows 98. In this parody program, Stephen Hawking (impersonated by an actor) calls Microsoft tech support to complain about the quality of their products.
Jimmy Carr – Stand up DVD. Jimmy Carr claims to have written a letter to him from his (fictional) 9-year-old son. According to Carr, Hawking paid for a free balloon ride for Jimmy's fictional disabled son.
Symphony of Science. Clips of Hawking are used in the first and fifth installments, respectively, A Glorious Dawn and The Poetry of Reality.
Touhou Project. ZUN references Hawking in the comments for one of the spell cards of the character Eirin Yagokoro in Imperishable Night, calling him the "wheelchair man". He has also released a song entitled "Future Universe of Wheelchair" on his album Magical Astronomy.
'Lollipop Chainsaw' In the video game, Juliet Starling berates Josey for 'making fun of Stephen Hawking' after he speaks through a voice box.