A popular fanon theory speculates that the Doctor and the Master were brothers, before Russell T Davies made very clear that it wasn't so. The show itself even poked fun of the clichedness of the theory in the new series.
Since the TV series has never revealed the various Time Lord renegades' original names, the fans who write fic about their lives on Gallifrey rely on the books' names for them: Koschei for the Master, Ushas for the Rani, and Mortimus for the Meddling Monk (the Gallifrey-era Doctor typically goes by Theta Sigma, his academy nickname from the TV series. Some fans apparently think it's the Doctor's actual name, which it isn't).
In the EU sections of fandom, it is almost universally believed that the Ninth Doctor's leather jacket originally belonged to Fitz.
Fix Fic for Donna's fate in "Journey's End" tends to rely on the premise that removing (or blocking, in most of these fics) Donna's memories didn't undo the meta-crisis. And since alt!Ten can't regenerate - well, the regen capability had to go somewhere, didn't it? Cue regenerating!Donna fic galore.
In Star Trek, fanon stated that Mr. Spock was the first Vulcan in Starfleet, though this isn't backed up by anything on screen.
Another thing the fandom agrees is that, because of their telepathy, Vulcans avoid physical contact like the plague, even though Vulcans on-screen have shown no qualms about touching or being touched. In fact, The Original Series established that for a long time it wasn't general knowledge among Vulcans that all Vulcans could mind-meld, and it takes training and concentration to be able to do it. Therefore, accidental touch-telepathy is not a thing.
Spock being the first ever Vulcan-human hybrid (to live to adulthood) is not actually confirmed in canon, but you wouldn't know it from the fandom.
Also on Star Trek: Lt. Sulu was originally only given one name, but the fans came up with a first name for him: Hikaru. This name was then used in the sixth movie, thus turning Fanon into Canon.
Ditto with Nyota Uhura. It took almost 40 years before we heard that name on-screen (never mind that the name "Nyota" was suggested for the character by the very actress who played her — Nichelle Nichols)!
It's commonly suggested (often taken as fact) that Voyager's bio-neural gel packs, which arrange information in a similar manner to the human brain, are the reason Voyager's holograms had a tendency to become sentient (while those on the Enterprise-D did not). However, it was never stated on the show.
Because alcohol does not affect Vulcans in the same way it does humans, fans often turn to chocolate or copious amounts of sugar when they need to get Spock drunk. This does have some deuterocanonical basis, as it shows up in the Star Trek IV novelization as an explanation for why Spock spends most of the movie acting loopy.
Sources to base fanon on are quite popular in the Star Trek fandom. This shows from how they've erected two big wikipedia-clones: "Memory Alpha" for canon information and "Memory Beta" for everything licensed, but non canon. On the date of this writing, Memory Beta has well over 41,000 articles, 6,000 more than Alpha.
Despite the fact that we've only seen them dating men, Olivia and Alex on Law & Order: SVU are claimed as lesbians by the show's large lesbian fanbase. Some of these fans were outraged when, in the episode "Ghost", Alex told Olivia about the man she'd been seeing. The term "manvil" was coined to describe the show supposedly dropping anvils that Alex likes men. Said accusation neatly ignores the possibility of bisexuality, but as always Subtext is where you find it. And of course, it wasn't nearly so bad as Serena Southerlyn's last minute coming out.
Word Of God declared that there was, in fact, UST between the two women. The actress who plays Alex basically admitted that something was going on:
Stephanie March: I'm not saying we're not... I'm not saying we're not in love.
Another common piece of fanon pertaining to Alex Cabot is that Liz Donnelly is her godmother/stepmother/aunt.
There's also the fanon that Spike absolutely hates his last name, Pratt. Admittedly, since he never mentions it and goes by William the Bloody, which was actually an insult, before going by Spike, it's logical.
There was a belief among some fans that "Buffy" was a nickname, and the Slayer's "real" first name was actually "Elizabeth". This has been Jossed—most notably by her grave stone, but there still seems to be a faction that clings to it (in the real world, "Buffy" derives from "Elizabeth" through the toddler mispronunciation "Ewizabuff").
After she came out during the fourth season, the fandom quietly decided that Willow had a huge crush on Giles' girlfriend Jenny during the second season. It's one of those things that just makes sense, what with Jenny inspiring Willow to start dabble in magic, the thing that later would become a not-so-subtle metaphor for lesbian sex. It is also canon that Willow has called Jenny her favorite teacher during that time frame. Given that Jenny was the computer teacher, she may have also inadvertently helped initiate Willow's hacking abilities too. Whether she had/has similar feelings for Buffy is debatable.
S8 makes it a little less debatable since Willow grills Satsu on what Buffy's like in bed (including how she sounds when she orgasms). Then she denies ever having a crush on Buffy to Buffy after telling Buffy to be careful with Satsu. Buffy in turn, almost petulantly, denies having a crush on Willow because Willow denied to Buffy first. Later on, in another issue, Kennedy starts showing jealousy telling Buffy, "But you put the moves on Red and I'll kill you like a chicken."
Willow: And just so you know... I never wanted to sleep with you either.
Buffy: What are you talking about?
Willow: I'm sayin' it's a good thing you didn't try your little experiment on me. 'Cause it wouldn't have worked, Summers. You're not even on my list.
Buffy: What list? There's a list?
Willow: Yep. And you're not on it. Not my type.
Buffy: Oh, yeah? Well, then, you're not on my list either!
Buffy: And other people too. Those are just examples off the top of my head.
Fanfic tends to portray Anya and Tara as best friends, since neither canonically had one.
Conventional wisdom is that Anya starting life as a human was a Retcon, but this was in fact part of the character from her first appearance. Giles refers in "The Wish" to the destruction of her power center making her an ordinary woman again. The original script, available on the DVD, included a line about her becoming Anyanka after she summoned a demon who cursed her.
There is also a common idea that vampires can choose "mates" from the humans around them. Not "mates" in the sense of turning someone into a vampire for companionship, but that a human can be bitten and marked by a vampire, thus taking a form of ownership over that particular human. This would, in turn, offer a sort of protection from other vampires, who would sense the mark, and leave that human alone. There is nothing, repeat nothing, in the Buffy or Angel series that indicates a vampire could do this, or would even be inclined to do so. They are much more likely to either kill or turn a person.
There's more fanon about Buffyverse vampires. Like that they have a psychic connection with the vampires they sire, which is sometimes true, but that only showed up once, and even then it was only in the form of Angel dreaming about the other vampire's kills; it didn't let Angel control him as it does in fanfiction. The fandom also seems to believe that a newly turned vampire is called a 'fledgling.' They are never once referred to as such in canon. Also, while vampires do get stronger with age, there's no particular point at which a vampire becomes a 'master'; it just seems to be a general term used for the leader of a large group of vampires, who is typically the strongest because vampires usually operate on Klingon Promotion and Asskicking Equals Authority.
On Gilmore Girls, the character Tristin repeatedly called Rory "Mary" as a nod to her innocent appearance and actions. In fanon, Rory and other characters often call Tristin "Bible Boy" though it was never spoken on-screen.
A popular theory is that after the series, when Rory was on campaign trail, she stopped in Philly to see Jess. Whether a platonic or romantic meeting, its a staple of most 'After Season 7'' fanfics.
With 500+ significant characters in 17 seasons, Power Rangers has a fairly hefty showing of this, to the point where some of the fanon actually conflicts with itself, and not just canon. Rangerwiki, a PR Wiki, has a list of some of the more common instances of fanon.
One notable example of PR fanon becoming canon happened in 2002: a long-time fan began writing for the show in its tenth season, and made multiple references to an older fandom-wide missing episode hoax in a pivotal episode, suddenly canonizing the hoax's storyline... though as Linkarapoints out, it probably would have a) not explained everything and b) sucked.
Some of the more popular bits of fanon are:
Billy's last name (he was never given one in-show, but the fans made it up, and when the official website was put together, they just threw it in).
After the death of actress Thuy Trang in 2001, the fandom has generally agreed that her character Trini Kwan passed away as well.
Z Delgado of SPD is the daughter of Danny Delgado of Wild Force.
One bit of fanon acknowledged by the creators is the idea that Operation Overdrive's Mack was created as a Sex Bot, to explain why Hartford would create a robotic "son" that's already an adult. According to Word Of God, concerns were raised about this during the show's production, but dismissed because Bruce Kalish didn't think anyone would be warped enough to reach that conclusion. He was wrong.
Somewhere between fanon, Actor Allusion and fandom inside-joke is the idea that Taylor (from Power Rangers Wild Force) and Tommy (from... well, everything) hooked up. This is because their actors were in a sex scene together on the MTV show Undressed.
There is a recent mounting wave of fanon locating the home of The Addams Family somewhere in New Jersey — sometimes in the midst of the Pine Barrens, sometimes in Edgewater, and sometimes in Charles Addams' own hometown of Westfield.
Heroes has accumulated quite a bit of fanon. Popular theories include:
Sylar has superhuman endurance, and also the Jossed idea that he eats brains.
Lyle is adopted.
Confirmed in a deleted scene from the first season; it may or may not still be canon. The on-line comics also mention that HRG and Sandra could not conceive a child.
Adam is the ancestor of most, if not all, of the Heroes.
Mohinder went to boarding school or to university in England, hence the accent. It's also common fanon that his native language is Tamil (which makes sense, since this is the primary language spoken in Chennai, where he grew up) and that he is an atheist (arguably implied in the comic "Monsters", but contradicted at several points on the show) and a vegetarian (this one has some support; the Heroes Wiki notes that the religious symbols at Chandra's funeral imply that he is a Vaishnava Hindu of the Sri Sampradaya sect, and most of them are [traditionally vegetarian] Brahmins).
Nathan is eleven years older than Peter (his exact age is unknown, but presumably he's at least 35 in the "Five Years Gone" alternate future to make him legally eligible for the U.S. Presidency; Peter is stated to be 26 as of Volume 1).
Mohinder's unnamed mother tends to be called Anjali in fics.
Sylar's original ability of knowing how things (such as watches) work has the side-effect of allowing him to always know the exact time.
Elle is the mother of Sylar/Gabriel's son Noah in the future. While it's widely recognized that it's not technically canon, few realize it's not even hinted or implied.
Making Kid Noah a biological descendant of either (but especially both) creates not only time line, but casting problems. The actor appeared to be about five to eight years of age when Knox kills him. Yet, if the Exposed Future is four years after the Volume 3 Present, then how did Kid Noah grow from an embryo to a very-mature three-year-old in that little time period? Then again...
Many Firefly fanfics have River referring to herself exclusively in the third person. This only occurred on two occasions in canon, one of which was in sarcasm.
The fans are adamant that Book was a former Operative, to the point of decrying The Shepherd's Tale which says otherwise, and many people considering it non-canon.
Likewise, the belief that River's parents knew what the Academy was and had been either paid or coerced into sending her there, possibly even having conceived her solely for that purpose, is fairly widespread. This is implied in the episode "Safe", where River is shown to be The Unfavorite and they brush off Simon as imagining things when he shows them her coded letters, but it's never directly stated and it's possible they really did believe nothing was wrong, or else realized Simon was right but were too afraid of losing their money and status to do anything about it.
A common fan theory is that Zoe refused to got out with Wash until he shaved his mustache, or that she made shaving it a condition of further dating/marriage.
Battlestar Galactica fans have been known to take a deleted scene where Elosha refers to a jealous god starting a war on Kobol as canon — despite it being, y'know, deleted — and thus extrapolating that the Thirteenth Tribe were monotheists. The most current Word Of God is that they were polytheists like the others (as evidenced by their Temple of Aurora), and the exodus from Kobol was the result of man "stealing fire" from the gods by creating life. The last five survivors of the Thirteenth Tribe became monotheists after meeting the monotheistic Centurions.
There was also a very common misconception that Tigh and Adama had served together during the First Cylon War. This was actually shown not to be the case in Season 2, Episode 1, Scattered. They met years after the war, on a freighter. It apparently didn't register with many fans, which is why there was a general uproar when Tigh turned out to be a Cylon.
No one's ever said there are twelve Lords of Kobol, but it's taken for granted by many a fan. Given that they've mentioned gods outside the traditional twelve Olympians and have only used "Lord of Kobol" as a synonym for "god", not a subset, there are probably more than twelve. The Caprican establishes that Illumini, the second major city on Gemenon, is built around a huge pantheon devoted to dozens of deities.
In the Original Series episode "Lost Planet of the Gods", it is explained that the Lords of Kobol were the leaders of that highly advanced civilization until they are wiped out in a vaguely-mentioned ecological disaster. Long afterward, they were deified by their descendants, the inhabitants of the Twelve Colonies. The last Lord of Kobol was the Ninth Lord of Kobol, into whose tomb Adama enters looking for a map to Earth (which he finds, and which is then immediately destroyed when the Cylons attack Kobol). Side-note: In order to enter the tomb, Adama uses his Council of Twelve Badge of Office as a key. The other surviving Council Members also had them, but didn't seem to realize their true significance, and Council Members elected after the Destruction didn't have them.
Leah Cairns (the actress who played Racetrack) mentioned in several interviews that she believed her character had Unresolved Sexual Tension with Helo (who was a former Raptor pilot himself), and that she purposely played Racetrack in this mindset during the show. It's never been overtly suggested what's going on between Racetrack and Helo (even though there are a couple of broad hints), but most fans consider that fact canon.
This particular example is fanon becoming quasi-canon. Cairns was shown a Racetrack/Helo fanfic, and found the idea of her character having Unresolved Sexual Tension with Helo hilarious... but also interesting. So she threw that characterization into her performance.
About half of the episodes of Highlander: The Series are set in an unnamed city in the Pacific Northwest. Fans unanimously referred to this city as "Seacouver" (a portmanteau of "Seattle" and "Vancouver") but this was never explicitly stated on the show itself. The "Watcher CD" given away with VHS box sets (and, later, the DVD extras) finally made this name official.
Methos, a 5,000 year old Immortal, was shown for his first few appearances on the show as a somewhat hapless, normal kind of man who just happened to be really old. However, at some point the writers must have caught on to the fact the characterization was incongruous based on his canon age and probable life experiences, because several episodes in Season Five established him as having a dark past. Fans ran with this interpretation, often ret-conning Methos’ earlier actions and behaviors to make him a far more complex, morally ambiguous and - arguably - interesting character than was initially supported by his actions in Seasons Three and Four. It’s also basically fanon at this point that Methos is bisexual. Most fanfiction about Methos involves at least some elements of this interpretation of the character.
Fanon for The Lone Gunmen can be traced back to a handful of very old fanfics. These include: the idea that Langley used to be addicted to drugs, and giving him the nickname "Ree," the speculation that Frohike had served in Vietnam as a sniper, and that Byers was a widower. Another fanon element defiantly ignores the aptly-named episode "Jump the Shark" to state that Fletcher was lying through his teeth (with the Gunmen's strangely OOC behavior being offered up as "proof") and/or that the Gunmen faked their deaths.
LOST fanon is mainly theories that become so widely accepted that they're taken as canon. Of course, this is generally because of massive hints. Jacob's nemesis being the Smoke Monster, and Richard being first mate of the Black Rock are all common.
Season Six tells us yes and no, but close on those two (Richard was actually a prisoner on board the Black Rock).
Some fans have taken to calling the Smoke Monster Esau, after biblical Jacob's older brother. This may be Better Than Canon since the Man in Black's name ended up being, essentially, "Hey You".
As per his original casting call (and confirmed later by Kristin Dos Santos), his name is meant to be Samuel, although this is never properly stated.
Alias fandom became eaten alive with various pieces of fanon that rapidly became totally disconnected from the actual characters and events seen on the show, especially where Irian Derevko was involved. Many of these were ship-linked, but not, and enormous fury was unleashed when it became clear that the series had no chance of following the path the fanon assumed.
Supernatural: fanfic featuring Anna before she became human will almost invariably call her 'Anael'.
It's surprisingly accepted that Dean was either sexually abused (by someone else, not John) or at least used sex inappropriately when he was younger. Hell, even his actor thinks he whored himself out to pay with the bills.
The brothers have been Mistaken for Gay on multiple occasions, denied it, and have had numerous heterosexual relationships. Fandom is convinced that they're not only gay, that they're only gay, and they are interested in each other. This was directly jossed by canon in a Fandom Nod, yet it hasn't stopped the shippers. Then again, this is the same fandom that believes the actors themselves are dating, to the extent of believing that their longtime girlfriends, now wives, are both The Beard and hired by CW marketing.
There's a difference between the Fandom and the Fan Dumb. A much more popular theory is that Dean is a closeted bisexual. Be certain of hearing about DoctorSexy.
I once read a review of a fanfic where the reviewer said that "Dean wouldn't be able to call Sam 'Samantha' anymore". As a matter of fact, Dean has never used that particular insult outside of fanfics (and not this one, other ones). Apparently this meme got to the point of the reviewer thinking it had happened in the show.
Fans of Merlin generally assume that Gwen's mother is dead (often she is said to have died in childbirth, to parallel Ygraine) and that Merlin was named for the falcon. They also sometimes use 'Ambrosius' and 'Myrddin Wyllt' as some of the 'many names' for Merlin mentioned by the Dragon. And whether Gaius being Merlin's uncle is this or, Word of Actor (Richard Wilson believes Hunith to be Gaius' sister) or Word Of God is a matter of some confusion.
Also, some fans say that Merlin is a warlock and not a sorcerer because he was born with his powers, and sorcerers have to learn magic. This is because Merlin is referred to as a warlock in the show, but all others are called sorcerers (some fanfiction has him angrily defending himself against accusations of being a sorcerer on these bounds). However, it's never addressed in the show, so we don't know if that's canon or not.
The existence of 'real' Arthurian legend also provides a huge source for fanfics, such as Mordred being Morgause's son.
Glee is one of the few shows where "This episode sucks because it violates canon!" could be a valid complaint, since the show is infamous among the fandom and critics alike for its on-again, off-again relationship with continuity. That said, it doesn't keep the fans from coming up with stuff that was never revealed in canon:
Strangely common in fanfic is the idea that QuinnFabray is a brilliant pianist. Occasionally added is the idea that her parents sold her beloved piano after she became a Cheerio.
Kurt and Puck adore Harry Potter. If one of them only shows up in a fic once, it will be to agree with the other one that HP is totally awesome.
Warblers Wes and David are more or less crazy. Sometimes, they are also utter failures when it comes to matchmaking.
Up until Kurt mentioned in The Sue Sylvester Bowl Shuffle that he still lived at home, the fandom generally assumed that Dalton Academy was a boarding school.
The name of Puck's little sister is as of yet unknown, but lots and lots of fanfic writers call her Sarah.
All the others call her Hannah.
At the end of the only episode Kurt's car has shown up in, Kurt tells Mercedes that his dad took it away from him. That was almost two seasons ago, and the car hasn't even been mentioned since then. Still, there are very few, if any, Kurt-centered fanfics in which he doesn't have his car.
How else would he get to Westerville and back? If someone else was dropping him off and picking him up, s/he would have to drive an hour and a half each way, making two trips. Six hours of driving each day.
Two about Dave Karofsky: he's a math nerd/whiz (from his father mentioning he was an A and B student, and his taking Calculus even as a high school junior) and he's a terrific singer (from Will's compliment in Sue Sylvester Shuffle and the fact that Max Adler is the only actor who plays a student who's actually been in a real glee club).
Dave is also almost always an only child and quite commonly, his mother is dead/gone (which is almost certainly based on the fact that during the two meetings with the principal and Kurt and Dave's families in Canon, only Dave's father has been there and there is never any mention of a mother.)
He mentions his mother in "On My Way". She may have been working at the time.
If Blaine's aspirations are brought up in a fic, they'll almost invariably center around law, medicine or teaching.
Many fans believe that the reason Blaine is in the year below Kurt isn't actually that he's a year younger than him. Their theory is that when Blaine was attacked after the Sadie Hawkins dance that he mentions briefly at one point, he sustained injuries that were severe enough that he had to repeat a year.
Law & Order's Serena Southerlyn is every subsequent female lawyer's fabulously bitter/sarcastic/promiscuous best friend. Particularly prominent in SVU Alex/Olivia fics, it must be said, proving the age-old trope that beautiful blonde ADA Birds of a Feather will be stuck together in fanfiction.
Abbie Carmichael seems to be gay in a terrifying number of fics, considering how conservative she was, and the fate of her successor (you sort of don't care if she's paired with Olivia Benson).
It was very, very well accepted fanon that Olivia was at least bi. This was given a Fandom Nod, then promptly Jossed.
Parts of the iCarly fandom are quite convinced that Carly and Sam are lesbians based on many moments between the two.
In Victorious fanfiction, Jade and Beck often reveal their full names are Jadelyn and Beckett. There's been no indication in canon that their names are anything but Jade and Beck.
Sheldon of The Big Bang Theory displays classic signs of Asperger's Syndrome, but the creators have shot down that idea. It doesn't stop the fans from making this guess though.
One bit of widely accepted NCIS fanon is that Ziva was raped at some stage, most likely multiple times. Somalia is pretty much the epitome of Ziva going through hell.
She was an attractive woman, tied up in an all-male camp of violent terrorists who enjoyed hurting and torturing her, and saw her as less than human. It's not exactly jumping far to get to that conclusion.
Especially since she still refuses to talk about it.
Up until it was confirmed in season eight, it was very well accepted that Abby's father was dead, even though both of her parents were mentioned in present-tense in the pilot.
In The West Wing fanfics, C.J. calls Josh "mi amore" (a one-off pet name) regularly and very frequently.
It's basically considered a given that in the future, Sam becomes the President and Josh his Chief of Staff. Writing a story that implies or outright says this didn't happen is tantamount to AU (however, this future is strongly implied/foreshadowed in canon, so it's not just a fan bandwagon).
There's a widely accepted explanation for why the presidential election years in TWW are two years offset from when they are in real life (Bartlet was elected in 1998 and re-elected in 2002, as opposed to the real life elections of 2000 and 2004): in the show's universe, when Nixon resigned, instead of Ford succeeding him, there was a special election, the winner served a full four-year term, and things carried on as normal from there. This fits neatly into canon since no nonfictional presidents more recent than Nixon are mentioned on the show.
A strange mix of fanon and Fanon Discontinuity — in one episode, Leo states that he has only been friends with Jed for eleven years, but has known him for 32. Fans usually ignore this, partly because a contradictory statement that implied Jed was friends with Leo for 40 years just made more sense to the fandom and is taken as canon instead, partly because the whole "eleven years friendship, 32 years acquaintance" thing was never explained, implied, or mentioned again.
Chiaki went to college after the events of the series. Ryunosuke tells him to study for college entrance exams (and Chiaki complains) but he never expressed a desire to go to college - he considered traveling like Genta.
Most fans accept that Kotoha is the youngest of the Shinkengers but there's nothing in canon to state this. She could just be the same age as Chiaki, but he treats her as a little sister figure.
Kaoru is somehow related to Shun from Denji Sentai Megaranger. Both he and Kaoru's father are played by Masaya Matsukaze.
Some Gosei Sentai Dairanger fans believe Kou and Lin are married by the time of the "Where Are They Now?" Epilogue. This is probably based on Lin having photos of Kou in her house (he does not appear in person) but given the age gap of at least 10 years, and Lin's distaste at Kou hitting on her, it seems unlikely they would have hooked up.
Engine Sentai Go-onger: Hiroto and Miu are twins. Their Power Rangers counterparts are twins, but while Hiroto is acknowledged to be older than Miu (and looks much older) their ages are not confirmed.
Choujin Sentai Jetman: Fan opinion differs on whether or not Gai is really dead. The tie-in manga sequel states he is, but not all fans take it as canon.
Sugishita from Bakuryuu Sentai Abaranger is a wizard, time-traveller, or controls entry to different dimensions. Comes from the Dino Curry House being used as an Inn Between The Worlds in the Vs specials, but this appears to have been dropped as of Shinkenger vs Go-onger with the death of Sugishita's actor.
Ninja Sentai Kakuranger: The Kakurangers all have the same family names as their legendary ancestors: Ōhōri Tsuruhime, Sarutobi Sasuke, Kirigakure Saizou and Miyoshi Seikai.
Kaizoku Sentai Gokaiger: Marvelous was born and brought up on a pirate ship, or otherwise joined his first pirate crew while still a young child.
Tokumei Sentai Go-Busters: One bit of widely accepted fanon is that Masato Jin is Yoko's father. He is shown to have been a friend of her mother (with the implication of romantic interest) and be very protective towards Yoko, but the show confirms nothing either way.
Blake's 7: Vila is not dead. He fell backwards, therefore he is still alive.
Gan is from the planet Zephron - a piece of fanon so widespread it even appears in his Wikipedia article. He's usually a Gamma grade, though some fics have him as a Beta. A very common but now discredited trope had Avon as an extra-special alpha (Silver Alpha, Alpha-Plus...).
Kamen Rider Double: Shotaro was a petty criminal in the past. This is based on a flashback in one of the Jewel Dopant episodes to him running from Jinno when Jinno was a beat cop.
Ren Akiyama is the father of the little girl featured in episodes 5-6, because the doll her father gave her resembles Kamen Rider Knight.
Kamen Rider Kuuga: Yuusuke Godai is dead. Possibly a theory to explain his absence from Kamen Rider Decade, where the Riders who appeared in the movies were all implied to be the originals, except for Kuuga, replaced by his AU counterpart Yuusuke Onodera. This is because Godai's actor now considers Kamen Rider an Old Shame and does not want to be associated with the franchise.
Godai is confirmed to still be alive, but missing, in a spin-off novel - although Canon Discontinuity means he could still be dead in the TV/film universe.
Kamen Rider OOO: Chiyoko Shiraishi is related to Mako Shiraishi from Samurai Sentai Shinkenger, or (since Decade states that the Shinkengers' world has never had a Kamen Rider) is some kind of AU counterpart to Mako or her family. Both OOO and Shinkenger were written by Yasuko Kobayashi.
Most members of the Sliders fanbase tend to hold the fanon claim that the Professor Arturo who had his brain sucked out, was shot and left to die on an exploding planet in "The Exodus, Part 2" was a double of the team's real Arturo, who was left behind by the team (by accident) in "Post Traumatic Slide Syndrome". This is supported by producer Tracy Torme, who said in interviews afterwards that there was a loose plan to have the "real Arturo" be found when the Slider team return to the planet he was stuck on, but she was shown the door before she ever had a chance to put this plan into motion.
In post-Reichenbach fics, Sherlock sometimes dyes his hair red while he's pretending to be dead.
Sherlock's eventual reunion with John post-Reichenbach is normally after three years (as it was in the novels) and John either punches Sherlock, kisses him, or faints (depending on whether or not the person is a shipper and if they've read the originals).
John also seems to have a jam fetish.
Upgraded to canon (sort of): a jar labeled "John's Jam" appears on Sherlockology's "Silver Blaze" advent calendar.
Lestrade apparently got Sherlock off of drugs as a condition for letting him consult.
It's commonly accepted that the Holmes family is very, very rich. Many stories involve the "Holmes Estate".
Along with this goes the notion that the reason Sherlock needed help paying the rent is that before the consulting-detective business became lucrative, his income was from a trust fund which was under Mycroft's control.
John's father was either an alcoholic or a soldier, or both.
Lestrade has a young daughter.
John's leg injury was real, but not from a gunshot. Also he has recurring pain (and sometimes limited mobility) in his injured shoulder.
There's a recurring motif in fanart that John has the RAMC insignia as a tattoo.
For some reason, there seems to be a widespread joke/belief involving John and red underwear. In other words, avoid Tumblr on "Red Pants Monday" if you aren't a shipper. And apparently Martin Freeman knows about it, too.
Mummy Holmes is either an Alzheimer's victim or M.
SebastianMoran has not been mentioned or seen on-show, with the closest thing being a minor Mythology Gag. If you just went by the fandom, you'd think he was a recurring character.
In The O.C., fans think Alex's ex-girlfriend Jodie is an emancipated minor and also a lesbian The Casanova.
Babylon 5: Although not strictly speaking canon, the generally accepted theory is that Delenn went Beyond the Rim at the end of her life and joined Sheridan (and Sinclair) there.
Smallville: There is a reasonably prevalent theory that Lana is also a meteor freak with the ability to make everyone, or alternatively just Clark and other meteor mutants, love her in some form. Lana herself is typically unaware of her power.
Lex has mutant healing powers. It explains his quick recoveries, the fact that his constant brain injuries haven't killed him yet, and why he's so interested in meteor mutants.
The reason the sets are always different for Bodie and Doyle's respective flats every time we see them is that CI5 maintains a number of flats which it's agents live in, and they move their agents around regularly.
Doyle is moody, inclined to tears, and a vegetarian.
Bodie is a cold-blooded loner, had a terrible childood, had a hellish experience being a mercenary in Africa, was rescued from it by Cowley and therefore looks up to Cowley as a father figure. Depending on who's writing the fic, he may well have been raped during all this suffering. All of which is only based on the cannonical facts that he left school at 14 and was later a mercenary for some time.
Many fics have Claire pregnant when she died on 9/11 even though there is no canon evidence for it.
Also common is the idea of Claire having amnesia or faking her death on 9/11, fueled by the lack of a body being found (though in reality, many 9/11 remains simply can't be ID'd with current technology, so no body doesn't mean no death.)
It was fanon for a while that Mac's full name was Mccanna Boyd Taylor, Jr. after that was revealed as his father's name. However,that got Jossed in Season 8-his middle name is Llewelyn.
In the mini-series adaptation Horatio Hornblower, Archie Kennedy was mostly a Composite Character. In the books, there was a midshipman named Kennedy, appearing in one scene, there was another midshipman particularly tormented by Simpson and there was a sailor who had a fit during a stealth raid. Those are the only elements from the book cannon that were used to create Archie, plus he was given lines of other characters. (In "The Frogs and the Lobsters", he has Lt. Bracegirdle's speech about civil war, and in "Mutiny", he was kind to beaten middie Wellard, which belongs to Lt. Bush.) In the series, not much about his background is known, but some facts are intriguing. Lots of the fan fic stories focus on Archie's days spent at theatre, because he said in the series that he once knew Drury Lane as if it was his home. He also seems to love William Shakespeare since he quoted or paraphrased him several times. In fan fics, he's a total Bookworm who knows his Shakespeare really well. Jamie Bamber, his actor, said in interviews that he thought that Archie was a third son of Scottish lord, and fans have embraced this idea as well. His family also tends to be pretty screwed up.
The X-Files: "Dreamland" dealt with time paradoxes and body-switching. Everything gets set back to normal and the whole universe goes back to the way it was before the time rip — but Mulder's apartment is still cleaned up and has a waterbed, and Scully still has a dime and penny that were fused together by the warp in space-time, even though the events that caused both scenarios never happened. It could be explained that they weren't in the path of the snap-back. But how would time snap back for the whole universe then? A fan theory holds that the time loop in "Monday" later in the same season was triggered by the universe repairing itself and trying to get rid of Mulder's waterbed, the last remaining evidence of the paradox. This makes a surprising amount of sense when you watch the episode — the starting point for each loop is the waterbed springing a leak.