- A second season episode is named "Olivia. In the lab. With the revolver."
- There are a lot of shoutouts to famous scientists and science fiction authors.
- In one episode Charlie suggests that Olivia see psychiatrist Dr Katz. Must be some Comedy Central watchers on staff.
- A conspiracy theorist in "The Road Not Taken" thinks that the entire Z.F.T. conspiracy is caused by "renegade Romulans from the future here to change the timeline" - which is the exact plot of J.J. Abrams' Star Trek (2009) movie. The actor who played the conspiracy theorist is Clint Howard, and he played a similar (read "exactly the same") character in an episode of Star Trek: Deep Space Nine.
- At one point a copy of Arthur C. Clarke's novel Childhood's End can be seen on a shelf; it now appears that Fringe shares similar overarching themes.
- Leonard Nimoy as William Bell. Think about it.
- The pilot of is loaded with references to the movie Altered States in the form of Dr. Walter Bishop's shady history as a Mad Scientist. Both Bishop and the Mad Scientist in the movie both combined powerful drugs with sensory deprivation tanks and are naive cloudcuckoolanders with bad social skills. Even their last names are similar, suggesting that Bishop's character might have been inspired in part by Eddie Jessop of Altered States. Furthermore, Amy Jessop in Season 2 has the same last name as Eddie Jessop. Considering Blair Brown is in the cast, this could count as a marginal case of Actor Allusion. That movie was cited as one of the show's influences.
- And finally in the season 2 premiere we have X-Files references! First, one character is shown to be watching The X-Files immediately before he dies. Later, a senator makes an in-show reference to "X-designated cases," implying that both the X Files (as in what Mulder and Scully investigated) and "The X-Files" (as in the TV show) exist in the Fringe verse.
- And later in season 2, the episode "Northwest Passage," Peter meets a small-town sheriff who turns out to be something of a conspiracy buff. So much so, one of her deputies tells her, that "sometimes I think you want to believe."
- In 2x02, it's lupus.
- In Episode 1x07, Mitchel Loeb refers to "Agents Coscarelli and Scrimm," who are presumably named for horror director Don Coscarelli and actor Angus Scrimm. Scrimm starred as "The Tall Man" in Coscarelli's Phantasm series.
- People turning to dust like in "The Colour Out of Space".
- There's also Dunwich Hospital in the episode "Grey Matters" - and there's a Dr. West working there.
- The Simpsons Pez dispenser.
- Teenage sociopath who can control people and make them kill themselves... "You don't really have a plan, do you?"
- In "August", the Fringe team is shown pictures from throughout history that show that one specific man has always been present at major historical events.
- David Robert Jones is the real name of David Bowie. Thomas Jerome Newton is Bowie's character (the alien) in The Man Who Fell to Earth.
- Olivia's license plate reads 1C3P01.
- Along the same lines, she had the nickname "Han" in high school due to being a loner ("going solo").
- Da-da DA-duh-DA-duh-DA-duh-dun
- The whole plot involving the time traveler in "White Tulip" is essentially the plot of Ludo's Rock Opera "The Broken Bride".
- Alternate Olivia's ringtone is "Science Fiction Double Feature".
- Astrid Farnsworth might be a Futurama shout out, or it might be a shout out to the real Farnsworth.* Almost certainly the latter...by extension if nothing else, since Futurama's Farnsworth is a Shout-Out to the good Dr. Philo.
- In 2x13 ("What Lies Below") the CDC shows Olivia a model for what would happen in the disease were allowed to spread. It shows it spreading over the whole world with infected areas in red and non-infected in black. Eventually the whole map is red...with the sole exception of Madagascar.
- William Bell and Thomas Henry Newton.
- A doctor in "The Plateau" mentions "nootropics". Olivia promptly pipes up "Smart drugs, right?"
- After failing to take the identity of a Daniel Verona, a man takes a pill to fake his death.
- The Fringe team finds that someone has dug something up out of a hole in a basement. Walter thinks it would be delightful were it a box with tiny legs that got up and ran away.
- Speaking of which, here's a somewhat far-fetched one from "Jacksonville"...This is one Ted Pratchett.
◊ Could this be a really twisted double allusion to the "trousers of time" theory? (Warning: the image is fairly disturbing.) - It could be a reference to this scene◊ from Planetary / Batman: Night on Earth.
- Speaking of which, here's a somewhat far-fetched one from "Jacksonville"...This is one Ted Pratchett.
- The glasses Walter wears in "The Firefly" are said to have been made by a friend of Walter's, a Dr. Jacoby from Washington state (who wore similar glasses in that show).
- "The Firefly" was the first episode in the Friday Night Death Slot.
- "6B" has Walter flipping a coin that always lands on heads. The hotel where this takes place is even named the Rosencrantz.
- Young Peter in "Subject 13" is seen looking at an original series Battlestar Galactica board game.
- In the second episode of season one, supersoldiers are grown from test tubes? Sounds like Space: Above and Beyond, another Friday Night Death Slot show.
- William Bell (played by Leonard Nimoy) used the alias "Dr. Paris" to operate on Walter. Leonard Nimoy's character in the original TV series Mission: Impossible was called "The Great Paris."
- Another Cortexiphan trial patient is identified as Cameron James
- Walter names a lab mouse John. This doesn't seem notable, until he reveals — literally; he'd turned it invisible — that he has a second mouse: Yoko.
- Amberverse David Robert Jones shows us the advantages of having one's body dismantled and reassembled at the atomic level.
- The creepy town of Westfield in "Welcome to Westfield" contains multiple references, including Silent Hill, The Walking Dead (2010), and The Crazies (1973).
- The victim from "Dream Logic" dies of acute exhaustion. He's from Seattle. Coincidence? I think not.
- At a crucial point in "Black Blotter", Walter goes on an acid trip that looks almost exactly like a Terry Gilliam interstitial from Monty Python's Flying Circus, complete with giant foot.
- Two undercover NSA agents named Hicks and Bowman?
- In order to get on Markham's good side in the rewritten timeline, Peter tells him that Olivia is looking for a copy of Gene Wolfe's Lake of the Long Sun.
- From The Cure (S1E06): "White is for Walter".
- The episode August (S2E08) has a few to Phantom of the Opera - an orphaned artist named Christine is kidnapped and a cymbal monkey is found in her kidnapper's apartment.
- The title of Letters of Transit (S4E19) is a reference to the classic film Casablanca and the central plot contrivance.
- At one point in the same episode, Walter exclaims "I am not a number! I am a free man!" From the same scene he also says "these aren’t the droids you’re looking for."
- At the beginning of "Brave New World: Part 1 (S4E20)," a Muzak version of Billy Idol's "Eyes Without A Face" can be heard when the man is getting coffee and then going down the escalator.
- The six-fingered handprint shown in the intro and during the episodes features a perfect duplication of the middle finger. It's a rare form of polydactyly, shared by another institutionalized doctor who worked with the FBI.
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