Doctor Who/WMG/Whole Series

Specific speculation on the Classic Series and/or the TV Movie goes into.

Specific speculation on the Eccleston era onward goes into

Specific speculation on the latest series goes into (contains spoilers).

Archived Jossed speculation for the final Tennant years post-"Last of the Time Lords" is in

Specific speculation of Matt Smith's first series goes into

Time War Monsters

 * The Could've-Been King was a great leader that the War erased from history. The Meanwhiles and Neverweres are other people who were unhappened.
 * Alternatively, the Could've Been King is another name for Omega. The vague shreds of evidence certainly lean in that direction, as pointed out by one troper already.
 * The Horde of Travesties were people whose very biology had been twisted by the changes in time, devolved and re-evolved in strange ways. They were, however, time-aware enough to know what had been done to them, that they were in the wrong bodies, and they couldn't cope.
 * The Skaro Degredations were obsolete--and often alternate--Daleks used as cannon fodder.
 * The Nightmare Child was the Master, post-End of Time. When he returned to the War he was still in freaky-hungry-energy being mode, and Simm!Master does tend to have a childish glee. I can see him eating Davros and Rassilon and anyone else he runs across.

One of the Characters is a Time... oh, wait.

 * A Timepiece? I'd have to say the clock from The Girl In The Fireplace, but the tower that got hit by the spaceship in Aliens of London also has a lot of evidence going for it.
 * Maybe one of the characters that isn't a timelord is a timelord?
 * As of the midseason six finale,
 * Maybe one of the characters that is said to be a timelord, actually is one?
 * Or maybe a Time Lord isn't actually a Time Lord? Maybe none of the Time Lords are Time Lords!
 * Shows you how much Doctor Who has entered popular culture.

The Nightmare Child was created through the power of both Timelords and Daleks
It's an uncontrollable, super power-ful black hole which destroys everything on its way.

The Roman priestess played by Karen Gillan in The Fires of Pompeii is actually Amy Pond
The Doctor could have thought back, realized he'd met somebody who looked just like Amy, and decided to create a stable time loop, dropping Amy off in Rome with specific instructions (while not sticking around himself, due to the timestreams-crossing thing). She could even have stayed there for a few weeks to adjust to the culture/her role in preparation for what needed to be done when 10 and Donna arrived.

The TARDIS is the same size on the inside
Everything that goes inside shrinks to fit, thus making the tiny amount of space in the TARDIS seem bigger. The Doctor just rolls with the "It's bigger on the inside" explanation because he doesn't get it either.

The TARDIS can regenerate 12 times, just like Time Lords
And we've seen it's regenerated three times so far - at the end of The Eleventh Hour, at the end of The Big Bang, and at the end of The Doctor's wife.
 * The console has changed in the classic series before (for example, in The Five Doctors) so it has probably regenerated more than thrice.

The Doctor is Santa Claus.
How else did he know about Rose's red bike when she was twelve? He said it in a fairly early episode, too, i think, so i don't think he went back in time without Rose just to check what present she got so he could mess with her.
 * I actually ran the Fifth Doctor's quote "A megabyte modem!" through the Bad Translator and got "Santa Klaus!" as the final entry. YMMV, of course...
 * Jossed by
 * I heard a crap theory once that Santa had a TARDIS. And I read somewhere else Santa hasn't invented a time machine, but if he invents one in the future, he can travel back and make sure everyone gets their presents in the past.
 * That means nothing. The Doctor's met himself plenty of times. If anything,

The Doctor is a Big Gay Panda.
Title spells it all.
 * Don't get it.

The Time Lords invented liquor to keep the Irish from taking over the universe.
Why else would liquor exist?

This is the only work of fiction in the past hundred years in which none of the characters is a Time Lord.
It had to be said.
 * Nope. Reg is Dr. Chronotis, isn't he?

The TARDIS is the house.

 * You know. That house. Think about it. She's potentially infinite in size, able to change her layout and appearance at will, is far older than should be possible be due to the Timey Wimey Ball, and associated with the color blue. She could also be said to contain a monster, if you want to be really hard on the Doctor--I'm not sure Eleven would disagree with the comparison.
 * Or, maybe House is House.

The TARDIS has always had a translator.
However, it was as broken as everything else in the TARDIS, and skipped some languages - like French. The Eighth Doctor finally fixed it. When he did, he used his psychic link with the TARDIS to route it through his head, learning 5 billion languages automatically. This also gave him total control over the translator, and makes it not work if he's comatose. Therefore, he can say anything he likes without it being translated. This also explains why Judoon isn't translated - the Doctor understands the Rule of Funny.
 * Come to think of it, this is proved by Masque of Mandragora. It does explain why French (in War Games) and Aborigine (in Four to Doomsday) were not translated, though.

The Doctor has been repairing the TARDIS over the course of the show.
Or it's repairing itself. Originally, he had no control whatsoever over his destination. Three and Four could get to the right planet (Planet of the Spiders and the Key to Time Arc). Nine and Ten seem to be able to aim, but can be a bit inaccurate (Unquiet Dead & Idiot's Lantern). The TARDIS repaired itself completely in Eleventh Hour, and is now in perfect condition. Any inaccuracy with specific times is due to it being an out-of-date Type 40 model. Also, Eleven is the first one with working stabilizers and brakes - previously, they were stuck, and that's why they made the noise. He leaves them because he likes it. Finally, Four never actually got rid of the randomizer. He merely adjusted it so he can use it OR choose a destination. That's why even with a working TARDIS, the Doctor has to ask where and when they are.
 * Even if he manages to fix it, it wouldn't matter too much. The one that decideds the destination is, according to the TARDIS herself, well... the TARDIS is the one that decides where the Doctor is going. Even if he doesn't want to.

One or more of the characters is a Time Lord.
Bear with me here. As You Know, the planet Gallifrey belongs to the Time Lords, who run the planet and do their Time Lordy stuff there. Now, as some sort of in-joke, Gallifrey cameos in several Doctor Who serials throughout the show's history. For example, the Ninth and Tenth Doctors occasionally mention Gallifrey by name, and way back in "The War Games" it's subtly implied that the Second Doctor's trial takes place there. From these references, it's almost certain that Gallifrey exists in the Doctor Who universe. Now, why is this relevant? If Gallifrey exists in the Doctor Who universe, so do the Time Lords. Logically, there has to be at least some Time Lords on this show. As for which characters are Time Lords? I'm...not sure, but if I had to choose one person, it'd have to be Mickey Smith.
 * Win.
 * Wait, what series is Gallifrey from originally?
 * Well, it involved a guy and his human companion traveling through time and space in a time machine disguised as a small 1950's phone booth. Oh, duh, it's from Bill and Teds Excellent Adventure!
 * Wait. Captain Jack Harkness can travel through time. He practically comes back to life every time he gets "killed", but while his face never changes, you can tell from the Rani and the Master that more experienced Time Lords can control the results of their regenerations. It's been theorized that a time lord can "eat" the remaining regenerations of another time lord thaat he's killed, or (far more reasonable) that the number of regenerations is merely a bureaucratic restriction and not some sort of "mana points". Since the time lords have supposedly been locked away in the Time War, their enforcement of the final death may not be in effect... And Jack's a rogue anyway, and a liar, so we figure he's probably not from the 51st century anyway, and quite possibly a rogue time lord. That thing he wears on his wrist must be a TARDIS, but it had the chameleon circuit break while he was in the 51st century. That's also how the blonde girl who's always with Mickey Smith or that northerner found a source of vortex energy on an entertainment satellite.
 * Obviously, Angel Bob is a Time Lord.

The missing serials from the Classic Series were lost in the Time War
The New Series Doctor claims to be 906 years old. However, he claimed to be over 1000 in the Old Series. If the Doctor is not lying about his age, maybe because of the Timey Wimey Ball, he lost some of his years. And it just so happens that many tapes from the original series have been lost as well. Coincidence? I think not.
 * Suddenly, my life makes so much more sense.
 * This means the Time War affected our universe as well. Steven Moffat, is this you?
 * Going by the fact that the only room for substantial gaps in time is Season 6B (due to him constantly travelling with human companions, i.e. Jamie)...and even then that's extremely unlikely to be nine decades...jossed?

The Doctor is the Discworld's Death.
The Doctor is Death; his House is his TARDIS, and Susan is Susan.
 * His domain is said to be outside of time, although IIRC never actually goes back, just slows and stops it. His favourite tools (the Scythe, the Sword, the Screwdriver...) give off a blue glow and slight hum and can manipulate molecules. He's officially supposed to be an impartial observer, but something about humanity has made him gradually grow more and more fond of it. And yes, he has a grandaughter called Susan. The First Doctor could have crashlanded on Discworld and taken up the mantle of Death. The only problem is that  has been Death since at least the creation of the Discworld, whereas Susan is still a child when he first comes to Earth - this implies that at least the First Doctor's tenure, if not all the Doctor's adventures so far, take place during one very long period of Death Takes a Holiday during Susan's infancy.

The regenerations keep getting more unstable.
The Second Doctor just shrugged it off. The Third spent some time in bed; the Fourth babbled about random stuff for a bit. The Fifth went into a coma for a while. The Sixth attacked his companion. Both the Seventh and the Eighth had amnesia. The Tenth went into a coma. His regeneration in "Stolen Earth" / "Journey's End" doesn't count because Ten stalled and redirected it. Later regenerations will be even nastier.
 * Alternatively, the regenerations were getting more unstable, but Jackie Tyler's tea fixed whatever the Gallifreyan council broke, and Ten will have it down pat when he has to regenerate for real. We know that Tylers and Ten both have special places in the new series.
 * This one seems to be supported by the latest regeneration -
 * I'm more convinced that this was to do with that specific Doctor's utter reluctance to regenerate having than it was to do with regenerations becoming more and more unstable. If the TARDIS is sort of psychic and gets inside your head, then it seems likely that a highly emotional reaction from the Doctor could have a knock on effect. This doesn't discredit the theory, though.
 * Ten's regeneration nearly but Eleven emerged with virtually no adverse effects. His may be the most stable regeneration since the first one.
 * This is also the reason for his getting younger. Every time the Doctor regenerates he's burning up his life force. His first form lasted him for nearly 400 years, but then he needed to regenerate, and it cost him a lot more than anyone realised. Basically he's either going to keep regressing, or he's eventually going to just fall apart at the seams when his body can't sustain the level of power drain it needs. This can also be an explanation for his regenerations changing personality completely, because his neural pathways are getting eaten away. He's trapped in a Body Horror cycle he can't get out of.
 * Alternately, the Doctor keeps regenerating into a younger body because he keeps getting older: he wants to at least appear young, even if he's anything but. Also keep in mind that the actor's ages haven't been a steady progression from old to young -- Peter Davison was 29 when he started playing Five, Christopher Eccleston 41 when he started playing Nine, Matt Smith 26, etc.
 * Considering that other Time Lords don't seem to have similar problems with regeneration (and have much more control over the result, if Romana is any example), maybe the Doctor has some kind of medical condition that interferes with it. Possibly stress-related, considering how his lifestyle compares to most Time Lords'.

The Doctor is not a Time Lord.
He's the future son of Haruhi Suzumiya and Kyon that inherited a mix of common sense and god-like power which he uses to traverse time and space doing heroics. He pretends to be one because it provides a good cover for his powers.
 * More fuel to "not a time lord" fire. Both Romana in the old series and the Master in the new have shown some control on who they become when regenerating. The Doctor never showed such control and was explicitly said to have none when regenerating from Nine to Ten.
 * On the other hand, once he was firmly Ten, he did figure out how to control regeneration; thus, his promptly regrowing a lost hand shortly after it got cut off, and more fun with that hand later.
 * The Doctor always regenerates as a result of sustained injuries; Romana and the Master (usually) regenerate on purpose. Also, in the old series, the Master had run out of regenerations, which resulted in him becoming a pile of blood pudding with eyes and teeth. (He got around it at the time by possessing others; since then, he seems to have acquired another Time Lord's body.)
 * The Doctor is not a TRUE time lord - he was born on Gallifrey and went through their ritual to become one, but he is not a true Gallifreyan like the other time lords. He doesn't know this, but it could explain his utter fascination with humanity as a whole.
 * Or he's "not a proper time lord" in the sense that Luke is not a proper Jedi. Maybe the people who run away from the Untempered Schism aren't trained to be full Time Lords (because the "enlightenment" you get from it allows you to comprehend time travel), and that's why he later went on to steal the TARDIS. This also explains why he's unable to describe how time travel actually works and his navigation of the TARDIS is so haphazard. Why are all the best heroes always school dropouts?
 * He's Wesley Crusher after Wesley left his apprenticeship with the Traveler. This also explains the whole "human on his mother's side" thing.
 * I never thought I'd see a theory which set Star Trek and Doctor Who in the same universe that would make me angry. Damn you.
 * A Time Lord? You'll never find any evidence to support that.
 * The Time Lords are all dead.
 * In Silver Nemesis, Lady Pienforte taunts the Doctor and Ace claiming to have knowledge of the Doctor's true nature. When Ace snaps words to the effect of "everyone knows that the Doctor is a Time Lord", Pienforte laughs and shakes her head. Not an actual denial, true, but maybe...

The personality of each of the Doctor's regenerations is influenced by the manner of the previous incarnation's death.
...Or alternatively, he subconsciously changes aspects of his personality to deal with aspects of himself that he doesn't like.
 * The First Doctor died from a combination of old age and the energy-draining effects of the planet he was stuck on; thus, he regenerated as a younger, energetic man with a penchant for running away.
 * The First Doctor was impatient and grumpy; he regenerated into a friendlier, more avuncular character who got along more easily with his companions.
 * The Second Doctor's forced regeneration at the hands of his government lead to a more forceful personality, a suave, debonair figure willing to cooperate, if grudgingly, with a government body.
 * The Second Doctor tended to panic and run away; he regenerated into a more proactive, calm, action-oriented guy, an incarnation who was not a Technical Pacifist.
 * The Third Doctor died after a long exile on Earth working for a paramilitary organization; the Fourth Doctor was a bohemian, anti-authoritarian renegade with wanderlust, who died sacrificing his life for the universe.
 * The Third Doctor was tired of being so attached to UNIT and Earth, and wanted to be more aloof.
 * Following a difficult regeneration, the Doctor became a reserved, quieter figure with an air of tormented nobility (Fifth)...
 * The Fourth Doctor was tired of being weird and aloof and wanted to have a closer relationship with Nyssa and Adric, for whom he was now responsible.
 * Even more alternatively, the Fourth was tired of running around and ineffectively dealing with people by offering them Jelly Babies. As a result, the Fifth became more of a... well-meaning sociopath - still doing good throughout the cosmos, but with far more consequences than a piece of candy (as explained in a much-further-down guess).
 * ...that died a long, protracted death after a more personal but still valiant, and very painful self-sacrifice. This lead to an extroverted, self-righteous, and obnoxiously colourful version (Sixth)...
 * The Fifth Doctor was tired of lacking confidence and presence, and wanted to be more impressive and showy.
 * ...whose sudden, accidental death brought about a clownish yet darkly manipulative persona.
 * The Sixth Doctor's moments of defeatism made him want to be more of a planner, a bit more optimistic, and a bit more realistic about his abilities.
 * The Seventh Doctor's very long period of clinical death lead to the amnesia and the Gothic Romanticism that partially defined the Eight Doctor's personality.
 * The Seventh Doctor's complex plans made him yearn for a simpler, more childlike view of the universe.
 * The Eighth's possible death during the Time War lead to the much darker and enraged Ninth Doctor...
 * The Time War was no place for an idealistic and optimistic Doctor, however effective he was; and so we get Nine, who is cynical and pragmatic in most things.
 * ...who, after sacrificing himself for Rose, regenerated into the Tenth, an individual very open to love with his companions.
 * Nine was deep in love when he regenerated and was never quite able to express it. He wanted to be someone loving and lovable, someone who would say what was on his mind when he wanted to, someone whom Rose would truly enjoy being around.
 * Season 4 spoiler: . This seems confirmed.
 * And
 * If this is true, then Eleven should be...aloof, calm and highly forgiving, like some weird hybrid of Three and Eight.
 * Or he should be torn in conflict between the impulse to save everyone and a distaste for violence. Oh wait...
 * Not long before regenerating into Eleven, Ten said that he would be proud to have Wilfred as a father, and the long, meaningful looks between Ten and suggests that she may have been . Perhaps because Ten missed his parents, Eleven came out younger to make people feel more parental toward him. In short, he turned himself into The Woobie because he misses his mummy and daddy.
 * I disagree because He will be a Jerkass this incarnation.
 * Not so much a Jerkass than suicidally overconfident and a thrill-seeker;  All these, plus   seem to indicate his arrogance and refusal to regenerate as Ten translates to a suicidal thrill-seeker mentality for Eleven, one who doesn't care for the rules and foolishly laughs in the face of danger in order to feel alive.
 * That makes sense, but it is also possible that Eleven is so willing to risk his life because he hates himself. A major clue supporting this theory is the Dream Lord. In "Amy's Choice", the Dream Lord keeps showing up in front of him as he is about to risk committing suicide with Amy. He may reason that if he dies, he will be rid of a genome that appears to be quite inconvenient if you look closely.
 * Alternatively - considering the above thought that The Tenth Doctor, it is not implausible that The Eleventh Doctor might regenerate as an Insufferable Genius with hardly any sense of empathy, similar to Sherlock Holmes.
 * Series 5 Spoiler!
 * So, how's the Eleventh Doctor reinvented himself from the Tenth Doctor?
 * He's come to terms and is more at peace with the Time War (or at least is willing to put it aside a bit more). There's no way the Tenth Doctor would, upon informing someone of the Time War, his role in it and it's effect on his life, would have been able to just leave it at "a bad day."
 * He puts his companions at arms length more, and is certainly more wary of romance with them. After losing Rose, the messy fallout with Martha (caused partly by his own self-pity and thoughtlessness over losing Rose) and even painfully losing Donna, his only non-romantic companion, the Doctor seems a lot more wary of the mess that comes with getting involved with his companions in that way. For himself as well as them; whereas Nine and Ten weren't particularly bothered about the effect of his relationship with Rose on Mickey, Eleven makes efforts to mend bridges as soon as he learns that Amy has a thing for him. Related to this, while Ten was a bit more confident and knowing about this sort of thing, Eleven is a lot more naive and clueless.
 * There's that vein of self-loathing alluded to in "Amy's Choice" -- a possible reaction against the cocky and at times over-confident Tenth Doctor, who ended up as a result getting within a hop, skip and jump of the "Time Lord Victorious" and full-blown A God Am I megalomania not long before his final end.
 * I could have sworn someone pointed this out already, but Ten spent some of his last moments shouting at Wilf that, essentially, he was more important and shouldn't be the one dying - now a major Berserk Button for Eleven is suggesting that anyone is unimportant.
 * I dunno, that's been a common trait for all three of the revival doctors. As far back as Father's Day minimum.

Related to the guess directly above: The Tenth Doctor's last words were partly an attempt at making Eleven less warlike and more cautious/self-doubting.
after  instead of, say, "Screw you, Daleks and Time Lords, I am locking this gate-of-eternal-Unpersoning for the good of the universe!" or "I just... Oh, wow, that was a lot of power... I always wanted to go to Barcelona... You know what? You were fantastic, Rose, and more importantly, so was I."

The personality of each of the Doctor's regenerations is suited to the adventures he is going to face
We know Time lords have some sort of temporal awareness so when the doctor "dies" and regenerates he uses that ability to craft a body/persona that will suit what will happen to him in the future. That's why the Doctor always wins and why his "renegade" personality is so different to other timelords. Time lords aren't perfect precogs however which is why some adventures are harder than others and why he eventually needs to regeerate again.

The Doctor is committing a form of suicide, though he's going to change the universe as much as he can.
Consider how long Time Lords live. Thousands of years and then some; in theory, "forever, barring accidents." The Doctor is burning through his regenerations at a speed that would be unfathomable to an immortal. Barring possible parts we don't see (especially the 8th/9th Regeneration and the Time War), it seems that his regenerations only last a couple of years each, as judged by the mortal companions he is with during.
 * Confirmed, at least in part, by Turn Left. In a world where the Doctor never met Donna, he died while fighting the Rachnoss, either not wanting or not thinking to get out alive.
 * There are numerous periods during which we don't see the Doctor's adventures, though: For instance, when he first left in Rose, after which we get to see some pictures of him in various historic moments, which clearly happened only after that because he had only just regenerated when he met Rose. The Sixth Doctor claimed to be 900, while the Seventh said to be 953, and those wacky episodes between probably didn't last 53 years. (Though if you add in the novels...) He could've spent countless centuries between the episodes that we've seen.
 * The Tardis Wikia site ties itself in knots trying to explain the Doctor's personal timeline, including the various novels, short stories and comics. They basically conclude that he's lied about his age, or forgotten, on multiple occasions, and the best we can say is that Ten is "about 1000 years old."
 * I quietly add 200 to the number the Doctor says in his head, making him 1,100 in "Rose" and 1,107 as Matt Smith. To me, it's like he's in denial about passing the Big 1-0-0-0.

The Doctor's real name is exactly that.
Hell, if even the Time Lords call him The Doctor...
 * I heard that he's called "The Doctor" because he earned the least, merest academic credential available on Gallifrey: the lowly doctorate.
 * Of course, it could be one of those ridiculously silly long names that "prove" a species is "advanced" that the closest concept/word in English is "Doctor." The Time Lords just use telepathy to "smush" it together. Is that enough air quotes, do you think?
 * Conversely, "The Doctor" could mean something entirely different in Gallifreyean.
 * Note that "The Doctor" doesn't work with Carrionite magic.
 * Hmm. I don't suppose maybe he could have some kind of an L thing going on, where ?
 * Alternatively. The Doctor is not his real name, but his real name was erased from time or otherwise removed, leaving "The Doctor" as the closest thing to a name he's got.
 * (Season 30 spoilers) Several of these theories are Jossed by "Forest of the Dead" -- River Song knows the Doctor's real name and uses it as proof of their future relationship; therefore, he does have a name other than just the Doctor, and he must know what it is. There's also the possibility mentioned below, that Time Lord names are ceremonial and are "lost" when a Time Lord abandons Gallifrey.
 * Issue #57 of the Doctor Who comic book reveals his name as " d³Σx2. Naturally, this isn't Canon, but it's worth mentioning.
 * The other Time Lord (err, Time Lady) whose real name is known is "Romanadvoratrelundar", or 'Romana' for short. It seems possible that the Doctor's real name is a similarly long and bizarre word beginning with "Doctor". That, or it starts with "who". Read this.
 * Compare Doctor Appleby from Jump Start.
 * His real name (or part of it) is John Smith, the one he usually uses for an alias. Or possibly.
 * Unlikely. "John Smith" was first used as his name when he was unconscious in "The Wheel in Space"; Jamie read the brand name off a medicine bottle and used it. Two kept it first for consistency and later because he liked Jamie. Three used it because Two did, and Four used it because Three did.
 * His real name is 'Rumplestiltzkin'. They say all myths are based in fact: HE was the origin of that particular story.
 * "I hate good wizards in stories: They always turn out to be him."
 * "Theta Sigma" was his nickname in school. Maybe that's his real name. (Some Fanfic treats it like that.)
 * I heard a kind of nuts theory once that he got the nickname "Doctor" due to an irregular heartbeat (listen to the beats of the opening credits - three sets of four, then a single set of three - like a double heart beat which was missing the final pump). Heard this theory from a friend and have been unable to find any confirmation for it online, though.
 * ...Wait. Isn't the drumming in The Master's head also from the theme song? Perhaps the time vortex gave The Doctor that same irregular heartbeat! ...Of course, considering The Doctor only gets his second heart until AFTER his first incarnation, there are some holes in these two theories...
 * Maybe not even the creators originally knew his name - he's always been the Doctor to them, they never actually gave him another one in the first place?
 * His real name is Doctor Who. End of the question.
 * Um, no. His name is not and has never been Doctor Who. No one even calls him Doctor Who, just 'The Doctor'.
 * Lots of the people who made the classic series, including the writers and the actors who played The Doctor referred to him as Doctor Who all the time, evidenced by the classic DVD special features.
 * Nope. He goes by The Doctor because that's what his original companions, Ian and Barbara, started calling him. He just kind of adopted it. However, it has been revealed that the Doctor actually invented the word doctor, which creates an ontological paradox wherein Ian Chesterton accidentilly created the word Doctor.

The Doctor is God incarnate.
Or a god incarnate, at least. He's clearly more than just another Time Lord, but they're at the apex of the technological ladder. Above them are only the various cosmic powers of that universe, gods in all but name; the Doctor is one of these. This not only explains how he can consistently defeat other cosmic powers, but also such other mysteries as the Morbius faces, why his true name is so secret, and various enigmatic comments from the seventh Doctor.
 * Amazingly, some variant of this would have become Canon if the show hadn't been canceled.
 * He is known as "The Lonely God" in Fanon.
 * In "New Earth," Novice Haim describes the "superstitions" regarding the Face of Boe: "...just before his death, the Face of Boe will impart his great secret, that he will speak those words only to one like himself... a wanderer, the man without a home. the lonely god." In Gridlock, The Face of Boe does die, and gives the Doctor a message - You are not alone.
 * While we're on that, actually, remember The Impossible Planet, anyone? "The Beast and his armies will rise from the pit to make war against God." Well...the Beast and his armies did rise from the pit, certainly. But I see only one man they made war with, and it didn't go too well for them.

The Time Lords' homeworld was, in a distant past, the world of Final Fantasy III.
As the Doctor explained, TARDISes are organic beings that are "grown". They are bigger on the inside, and can travel through space and time (so it could be argued that they don't exist between the time when they start traveling and their destination). All these properties apply just as well to FFIII's Fat Chocobo -- they can carry a large amount of items, disappear when not needed, and snap back to reality in different places (we know it's the same chocobo because it carries the same stuff). It can be concluded that Fat Chocobos are untamed TARDISes, and that the heroes from FFIII are ancestors of the Time Lords. They are immortal, barring accidents, can come back from near-death through regeneration, and sometimes change appearances (or Jobs), looking younger (like summoners) or older (like scholars). Their descendants probably inherited the ability to change appearance only through regeneration, as they were a mix between light warriors and mortals. Xande might also be the Master's first form.

The Doctor is a fruit fly
He likes bananas. Bananas are good.
 * This theory means that Gallifreyans evolved from insects.
 * Somebody needs to draw this. Now.
 * Like insects, Gallifreyans have a system of tubes for breathing instead of lungs.
 * Wait- Gallifreyans breathe through the Internet?

Unseen eons pass for the Doctor in several episodes.
An alternative to the suicide theory. We know the Doctor makes a habit of bidding farewell to someone, leaving in the TARDIS, and then immediately returning to invite them to be a companion. Examples: "Rose" and "The Lazarus Experiment". Here's what's going on: he leaves; he writes down the exact time and location, a personality profile of the companion, and the last thing he said. Then he goes off and does his thing for epic amounts of time; without Companions, he never gets killed. Eventually, he gets lonely, just as he knew he would, and he picks up one of the humans he's stashed throughout history pretending no time has passed. This also explains his inconsistent age - he's forgotten how old he's "supposed" to be. What a tangled web we weave when we practice to deceive, indeed.
 * Something similar explicitly happens in the Expanded Universe. The Eighth Doctor Radio Times comic strips all happened while the companion in the Eighth Doctor novels was at a pop concert, for instance. And in Canon, "The Face of Evil" reveals that he wandered off (in the Novelization, near the start of "Robot") and inadvertently created a megalomaniacal computer in the far future.
 * The Eighth Doctor Big Finish audios have him stranded for six hundred years on an ocean planet, with a broken TARDIS he doesn't have the proper tools to fix.
 * Also worth consideration are the periods that he travels without a companion (for example, between "The Deadly Assassin" and "The Face of Evil"; between "The Runaway Bride" and "Smith and Jones") or with only non-human companions (for example, between "The Invasion of Time" and "Logopolis"), making his possible age even greater. And there's the time skip at the end of "Doomsday": How much time passed with the Doctor moping around the universe until he got the idea to send his message?
 * Hopefully not long, otherwise the gap would have long since closed.
 * In "Rose," this would explain the various pictures that Clive shows Rose of his other adventures. He probably didn't have them before that episode because Nine had probably just regenerated (with the whole ear thing). So, after Rose says no, Nine goes off to the Titanic, to JFK's assassination, etc. and then comes back for Rose. Perhaps Nine had hundreds of adventures alone after Rose turned him down and then, one day, he suddenly slapped his forehead in a comic fashion, exclaimed "Of course! I should have told her that it travels in time as well!", and went back to the exact moment he left her to see if it would tempt her on board. To Rose (and us), it seemed like the TARDIS had only been gone a second; to the Doctor, it might have been ages.
 * This canonically occurs with a 200-year time-skip between "The God Complex" and "Closing Time", during which the Doctor gets up to the stuff we see him doing at the start of "The Impossible Astronaut" and at least two adventures with River Song (Easter Island and the Jim the Fish incident).
 * Not necessarily 200 years. Remember rule #1: The Doctor lies.

The TARDIS is a Weirdness Magnet.
Either there are scads of monsters and alien invasions everywhere in the timestream, or there's a reason the Doctor keeps running into them. Since the TARDIS can move freely in time and space, instead of attracting weird things to itself, it goes to them. The Doctor might even have programmed it to behave this way, especially if the slow suicide theory is correct. It would explain a lot of the "mistakes" he makes with setting the destination, such as going to 1879 instead of 1979 in "Tooth and Claw". The TARDIS may also make more subtle adjustments. If the Doctor wanted to take Martha to meet Shakespeare, he had a window of several decades; what are the odds of him hitting the exact day the Carrionites made their move?
 * There's a suggestion in one of the old Doctor Who monthly comics that the Tardis activly seeks out trouble - without letting the Doctor know of course - and deposits him where he can do the most good. This accounts for the huge number of Monsters of the Week AND why the Doctor often has trouble steering. The Tardis simply overrides him.
 * In "The Vampires of Venice," The Doctor takes Rory and Amy to Venice, Italy. They could go to there during any time period, and they get there when there is a vampire problem. What are the odds?
 * This one seems virtually Canon, but keep in mind that the Doctor and his companions don't get into trouble every time they visit somewhere: it's only the times they do that we get to see it onscreen. It wouldn't be very entertaining to have an episode where Eleven, Amy and Rory go sunbathing on a beach planet, for example. ... I'll be in my bunk.
 * Confirmed as of the "The Doctor's Wife". When the Doctor points out to the anthropomorphized TARDIS that "she" was never very reliable, the TARDIS responds that she always took the Doctor where he "needed" to go.

The Doctor and the TARDIS have a mild psychic link, and the TARDIS influences him to home in on weirdness when choosing a destination.

 * This is Expanded Universe canon -- it's in the book First Frontier.

The TARDIS is a cranky old thing that's sick of constantly traversing the universe; it repeatedly puts the Doctor in mortal danger just so he'll die already so it can have a nice rest.
The Time Lords were isolationist and rarely left the planet, and so it's unlikely that they built their TARDISes to withstand centuries of travel. And the Doctor's TARDIS was out-of-date even before he stole it.
 * Jossed by "The Doctor's Wife". If the TARDIS is to be believed, it "stole" the Doctor because it was tired of being stuck on Gallifrey and wanted to see the universe. The Doctor was the only Time Lord mad enough to take the bait.

The Sonic Screwdriver is Not What it Seems.
The sonic screwdriver is not a miracle piece of technology, but rather a conduit for the Doctor to channel his innate psychic power through. As seen in previous episodes, the Doctor has telekinetic and telepathic abilities, which take an intense amount of concentration to use, making them almost useless in high-stress situations. To compensate for this, the Doctor created the sonic screwdriver to focus his abilities into short bursts of psychic manipulation. This is not to say that the Doctor did not install some additional technology in the device to perform certain tasks, but if you notice, it never works as well for other people when they use the screwdriver.
 * Possibly Jossed by the Season 30 premiere, when  is seen to have a sonic screwdriver.
 * Yes, but does it work as flexibly and omnipurposely as the Doctor's? Yes, this theory has weight, especially after they introduced the "psychic paper," which essentially works the same way. The Sonic Screwdriver is a Magic Feather. The Doctor made it for himself, then erased his memory of doing so to give himself a psychological crutch to use his otherwise problematic Psychic Powers.
 * Note that Ten says in the Five/Ten Children in Need special that Five didn't replace his sonic screwdriver because he was showing off. Also note that, when Ten broke his own sonic screwdriver, he built a new one fast.
 * It's possible the sonic screwdriver does run on psychic energy because in season 6
 * No? Who? Amy? She's not part-Time Lord. She and Rory are 100% human..
 * Explaining time? *sigh*
 * Another possibility is that the sonic screwdriver is just an easy name; its real Gallifreyan name (unpronouncable or incoherent to humans and other primitive species) means something in terms of atomic/molecular manipulation, that, also as best as the TARDIS can translate it, is the Gallifreyan equivalent of a screwdriver.
 * When it originally appeared, it was used to unscrew screws. The ability of the device to do anything is a Plot Tumor.
 * You mean an awesome tumor.
 * Well, there is a reason they wrote it out of the show during Five's tenure in the old series. It didn't return until the TV movie. One of the first things they did on the new series was establish that it simply can't open certain things, just to keep it from being too easy.
 * Not especially. I don't think deadlocks appeared until the season finale.
 * The sonic screwdriver is far more powerful than a device of that size could normally be. They'd need to pack a lot of technology inside that little wand for it to do half the things it does. If only Time Lord technology could make things bigger on the inside...

The entire series takes place within The Matrix
Yes, the other Matrix from the one above.

The Doctor (connected to the TARDIS) is an alien computer program hacked into the Matrix by aliens. The reason he can regenerate his body, travel through time and space at will, and all that is because he has control over the Matrix. Now he, like the humans in the Matrix, doesn't realize what he's in, but the alien code making up his program means he can control it to a far greater extent than humans, or even most programs can. When he travels out through space and time, he's entering the Expansion Pack for the Matrix that the machines are creating for the humans in the Matrix to explore once their virtual world ages to the point where space travel is possible. At this point though, it has many buggy programs (evil alien creatures), and because the Doctor is fighting them, the machines have learned to turn a blind eye to the Doctor as his programming seems to make him inherently out to do good (and because he hasn't realized he's a program), though they are trying to reverse engineer him without him knowing and are trying to find some way to control or delete him (perhaps as part of this, they created the Master and the other Time Lord enemies for The Doctor? Alternatively, the other Time Lords are other programs hacked into the Matrix by the same or different aliens). The machines at a point even manipulate The Doctor program into destroying the bugs they need him to destroy the most by, say, throwing his control of the TARDIS off enough, or by messing with the random number generators in the Matrix enough to make it so that The Doctor always ends up where he's most needed.

The companions are humans in the Matrix, but every so often the machines get involved and Power Up a companion (like the Doctor Donna or when Rose looked into the time vortex) to help the Doctor defeat an especially destructive/bugged program. They immediately remove these program enhancements once these threats are over, hence why these companions all end up reverting to a purely human form afterward, often causing damage of some kind.

Travelling to alternate universe means traveling to back-up or older archived versions of the Matrix (or a past Matrix)

The Daleks appear to be especially dangerous bugs (perhaps created by another alien race hacking programs into the matrix in the form of Davros and company), seen by the fact of their Reality Bomb. As it would destroy all the "alternate universes", it would mean that the bomb was a bug/virus of such power and destruction to be able to shut down the entire Matrix, as well as all the backup copies! This scares the Machines so much that they go beyond even the powerups they gave Rose with the Time Vortex, and they actually try to turn Donna into/combine the human Donna with the code of The Doctor (essentially creating a Human/Software cyborg), as well as copying (imperfectly) The Doctor, in order to stop Davros and the Daleks. Once the threat is over, they quickly make the Doctor's knowledge start destroying Donna's brain, as they absolutely don't want a Program/Human combination running around, especially as such she would be both extremely powerful and would probably be a bizarre enough combo to realize what The Matrix is, even when the alien programs of Davros and The Doctor were unable to. Because none of the characters realize they're in the Matrix, they all rationalize away any bizarre coincidences, ret-cons, or continuity errors much in the same way the humans rationalize away deja-vu. Dalek Caan went insane not because he saw into the time vortex or anything like that, but because he realized what the Matrix is and that they are all trapped in it, but knowing no way out (and now insane) he just turns on the other Dalek and Davros programs.

The true hero of the series is the TARDIS.
This requires the following to be true.
 * 1) The TARDIS is not only alive but sentient.
 * 2) The TARDIS can detect time oddities and atrocities.
 * 3) The TARDIS desires to correct these.
 * Confirmed, confirmed, and (via an inference of Fridge Logic) confirmed as of "The Doctor's Wife".

Now, the Doctor is good at fixing this stuff, so the TARDIS just dumps him there and makes sure he fixes the mess.

The TARDIS likes Earth.
Related to above: she keeps taking the Doctor there to fix stuff. She certainly seems to enjoy being a police box.
 * Broken, remember? Then again, if she's as intelligent as we think, she might have deliberately stuck on the 'police box' setting just because she likes it.

The 1960s Movies are canon.
This explains why Bernard Cribbins is so excited about the Doctor. Clearly, there was some Chameleon Arch thing going on, but it can all be explained with a little determination. This also means he helped the Thals against the Daleks twice, thus getting the Daleks thoroughly annoyed.
 * When did Bernard Cribbens help the Thals against the Daleks? He's only in the second movie, and the Thals are only in the first.
 * No, The Doctor assisting the Thals twice, not Bernard. Bernard clearly portrays two separate characters. Unless he's a Time Lord as well. But then........ouch!
 * Excited? When they "reunited" during the Titanic incident, he just nonchalantly caught the Doctor up to speed about why central London is abandoned.

The TARDIS has some sort of device that draws attractive women to The Doctor.
The TARDIS is a chick magnet! Maybe it's trying to tell the Doctor something...
 * Some men buy fast cars to attract women. The TARDIS can travel almost instantly to any point in space and time.
 * What you mean, almost instantly? If I take five minutes to get my TARDIS from one destination to another, I can just set my destination for "the time that I just left" as well as wherever I want to get to.
 * The only frame of reference in which "instantly" even has any meaning when you're traveling in time is your own.
 * Maybe the TARDIS is a Covert Pervert, and getting a thrill out of the Doctor getting all the girls. And boys. That's why  Now that we know   it's quite possible. As to why, it could be because the TARDIS can't relieve tension the way we flesh beings do.
 * I'm not so sure about the 'TARDIS is trying to put the Doctor in a relaionship' part, but personal headcanon has a similar theory. The TARDIS knows that the Doctor needs his companions for mental stability. TARDIS also knows that humans don't live for very long, and therefore is helping the Doctor by arranging things for his companions to be not-so-human. Examples; Rose,.

The TARDIS translates not only for the Doctor and companions, but also for the audience.
And the TARDIS has a strange sense of humor, in particular a fondness for Fakesperian accents. And this explains the infamous "half-human" statement: it was a TARDIS translation error, and the Doctor meant to say that he was half Time Lord and half Ordinary Gallifreyan.
 * So the TARDIS is aware that there's an audience. That explains why it didn't translate the Doctor speaking Judoon into something we could understand -- it knew about the Rule of Funny.
 * Say, why doesn't it translate the Doctor's British vocabulary into American equivalents for Peri?
 * Her carelessness is half the reason for Five regenerating into Six. The TARDIS knew this (possibly even before it happened) and was a little angry at her.

James McCloud is The Starfox Universe Master.
Because he's too much like Eric Roberts, the Cat Nuns seemed familiar, and the final boss in the first two games was very similar to the Determinant from Destiny of the Doctors.

By creating a Generic Bad Guy that he based off of Davros, the Master was able to stage a "Wag the Dog" war against Venom so he could be seen as a Hero to the Cornarians when he kicked Andross' Kaled ass. Fortunately, James was betrayed by some pig and was destroyed before he could reap his rewards. Having worn out his regenerations, the Master went to the planet Sauria to steal the body of anyone he could find via that transparent shape-shifting snake ability he used in the movie. A metal imprint and a functional robot still remained on Venom complete with mind control powers, resulting in frantic hallucinations to any who dared trespass on his domain.

The TARDIS is the Doctor's Psychic Projection.
Heck, throw in the ol' Sonic Screwdriver while we're at it.

The Doctor is the TARDIS' Psychic Projection.
He allows the big T to interact with humans. The "regenerations" are just a rebooting and reset of the projector device.

The Master is compelled to see the Doctor as his enemy because he has No Fourth Wall.
The drumming sound in his head? It's actually the bass line for the Doctor Who theme. He is subconsciously aware that he is a fictional character in a fictional universe and meant to be a Designated Villain for the series, which the constant theme stuck in his head keeps reminding him of, and it compels him to fight against The Doctor and be evil. How did he get this way? By seeing into the rift that all Time Lords look into as kids, in reality a rip in their fictional dimension into ours; those who look into it either run away in denial of seeing "the real world", go mad upon realizing they're nothing but fictional constructs, or become Dangerously Genre Savvy (AKA "inspired") as a result.
 * When the Master looked into the vortex as a kid, he saw the Doctor Who opening credits, and it drove him mad. Imagine looking through a rift in time and space and seeing Colin Baker's terrifying disembodied head flying toward you. You'd vow to kill that guy, too!
 * Speak for yourself. Colin Baker is BADASS.
 * Jossed. The sound's a white point star emitting a signal to take Gallifrey out of the Time War. Rassilon sent that message through the rift.

The Doctor will meet a copy of himself calling himself "Doctor Who" in the future.
That "Doctor Who" will have his own "infotainment" show, his own TARDIS, and a Dalek companion that he tortures regularly. And he will in fact be the Valeyard, given his own life through one of the Doctor's trips into an alternate universe (E-Space, the Parallel World of "Rise of the Cybermen/City of Steel/Army of Ghosts/Doomsday", the alternate universe ...), and given his own regeneration cycle opposite of that of the Doctor's (the Doctor's 10th regeneration is the Valeyard's third or fourth, for example).
 * This has already happened in the Expanded Universe.

The Whoniverse's Earth is not that of our own.
Our Earth is in fact a primitive Gallifrey. On the Avatar: The Last Airbender page, there is a guess stating that that earth is primitive Gallifrey. Also true. There will be a nuclear holocaust in the far future that will mutate the surviving humans so that they have bending powers. Reincarnation will be channeled into one being, the Avatar. The Avatar's soul is made up of four different benders, each with a different bending type, who were all going to be reincarnated, but became one being because of even more mutation. The Avatar will then become the first Time Lord, and so on and so forth. Our Earth is the H2G2 Multiverse whole-sort-of-general-mish-mash Earth, and changing Earth enough to make it the earth of Avatar: The Last Airbender will effectively make it an entirely different planet, one that will someday be called Gallifrey.
 * Unquestionably Jossed. For starters, the Gallifreyans were one of the old empires that fought the Great Vampires and Racnoss eons ago. Also, why would the Ninth Doctor be so redundant about mentioning the death of his own planet in "The End of the World"?

The Whoniverse Earth IS our own, and the Series 3 climax definitely happened.
When the countdown happened in "The Last of the Time Lords", you can't honestly say you didn't start thinking, "Doctor. Doctor. Doctor." You know you did. The number of people watching that episode was equal to or greater than the number of people left alive at that point, so the trick worked. Unfortunately, not just the time of Saxon was erased, but all the obvious alien encounters we'd had up till that point.

Due to his constant and repeated visits throughout time, the Doctor's Weirdness Magnet has been imprinted onto Earth and on humans themselves.
While instances of aliens arriving when the Doctor is present exist, there are just as many if not more instances of aliens being present on Earth or around humans long before the Doctor arrives, sometimes for centuries or more. This is due to Earth itself and its inhabitants acquiring the same attraction for weird shit as the Doctor through osmosis; his far more potent magnet is required to trigger the events, resulting in many examples of aliens making their plans for conquest or otherwise, but not executing them until the Doctor arrives.

The series is in the Planescape multiverse
The "Arcadia" and "Elysium" that the Doctor mentions as battlefields of the Time War are actually the Outer Planes Arcadia and Elysium. Besides that:
 * They have thematic similarities of exploration, wonder at the infinite, and weirdness
 * The Doctor used Clap Your Hands If You Believe at the third season finale
 * The Lady Of Pain must have a colony of Vashta Nerada living in her shadow
 * The Nameless One is a Time Lord with a really weird regeneration process
 * The Weeping Angels are a very Planescape-y threat (the monster manual supplements for that setting are /weird/)
 * The void that he banishes the Daleks and Cybermen to could be the Astral, or maybe the Ordial
 * "The Elemental Plane of Ash" is a phrase I can easily imagine rolling off David Tennant's tongue
 * The TARDIS is already shown to be able to travel to other realities (at least if the Time Lords are still around)
 * A TARDIS powered by a spelljamming helm, despite the fact that that's probably not the case, would just be awesome

(There is almost certainly more evidence in Old Who.)
 * While Nameless One's whole story makes him unlikely to be a Time Lord, he is one of those wrong fixed points in time, much like Jack Harkness.
 * His namelessness exists for the same purposes and by the same method as the Doctor's.
 * Ravel is a Time Lord. She's been mazed by the Lady, but has apparently been outside it several times, despite mazes collapsing after their prisoner escapes. Actually, she hasn't left(or her "maze" is actually her TARDIS), those are just other regenerations that all showed up in Sigil at the same time because she's a Stalker With a Crush. And she's pretending to be a Night Hag.
 * And she's every "night hag" ever, all pretending to be different people. The Night Hag is actually her renegade Time Lord name, similar to the Doctor, the Master, and the Rani. Because everyone is a Time Lord.
 * Continuing with this idea, Ood are the original stock from whom the mind flayers evolved. Let's face it, they have an elder brain a central consciousness shaped like a brain, and they come with psionics and tentacles. We can therefore assume aboleths are what happens when a species derives from a Jack Harkness fixed point, given their near-immortality (but watered down from the first, Piscaethces the Blood Queen, by removal of the automatic return to life when killed).

Timelords are a Nemesis Plot

 *  It seems he's doing a pretty good job.
 * No, Nemesis himself is a Time Lord. The Seventh Doctor did drop off Ace on Gallifrey because he knew that she would be sent back to the beginning of Gallifreyan history and become the mother of all Time Lord society, thus making them more aggressive and able to resist the Daleks. Ace, who we know from the Expanded Universe to be sexually adventurous (even if it never happened on-page, Benny said it flat-out) not only made the Time Lords aggressive enough to fight the Daleks but also altered the doctor's DNA so that he would be more open to interspecies romance. When the Time Lords were destroyed in the Time War, the Doctor realized his mistake and used the Key to Time...

Top Gear is a Doctor Who spin off show in the style of a Car Magazine show
The Stig is obviously a Timelord; he's even regenerated once on the show already from Black Stig to White Stig. He has access to aircraft carriers and military equipment, obviously through UNIT, and The Sixth Doctor (looking a bit different due to the Timey Wimey Ball) and the Daleks have made crossover appearances. Jeremy Clarkson must be Davros in disguise.
 * Christopher Eccleston and David Tennant have also made appearances on the programme. Eccleston's appearance also featured the car he was driving phasing in a la the TARDIS. Hmm...

The Master exists in this universe, and he is Philip Zimbardo
Look at this guy or his wiki or his prison, and then consider the fact that he's a social scientist who continually performs experiments upon people in the name of science. Someday, a blue police box will be spotted on the campus of Stanford University.
 * Zimbardo once wore a cape to a psychology conference. That's some serious Ainley!Master fashion sense right there...
 * A CAPE?! Oh my god...mad scientists are real... Woohoo!
 * Just look at the titles of his books -- The Lucifer Effect and The Time Paradox are excellent titles for Who-pisodes.

The Doctor Changes History Quite Often
He likes to protest that he's not there to change the course of history, he's dismissed others' deliberate attempts as "time-meddling" or just plain doomed - and then there were the events of "Father's Day". Changing history bad, right? Not something he'd do?

On the other hand, he changes history almost every episode. He dinks around the universe through various time periods, and often in the course of those travels, he tries to save lives and stop various threats, even bringing down entire societies. This can't help but change history.

This serves to explain matters like Zeerust-ed glimpses of the future from past episodes (including why Zoe's early 21st century doesn't look much like Rose's) and inconsistencies like the UNIT dating controversy. The Doctor's travels (and those of other time-travelers) have altered galactic history quite a bit. As the Doctor seems to take a special interest in Earth and humanity, his interventions in particular have drastically shifted human history many times.

Perhaps because he's a Time Lord (or perhaps out of simply greater knowledge), he's capable of changing history without summoning Clock Roaches every episode. Or perhaps simple changes in history don't endanger reality, and the events of "Father's Day" arose from other circumstances related to the change - such as his being a direct witness to his changing history.

The Doctor tries to keep the memorable bits of human history consistent (the Aztec Empire, World War 2, etc.), but sometimes things change (Zoe's world shifting into Rose's world) and he doesn't entirely notice or care enough to spend time fixing them. Sometimes, he notices the changes (like the loss of the vast human empire that he expected to see in "The Long Game") and for whatever reason, he doesn't have the resources to fix them.

And sometimes, he decides to change history with six little words because he feels like it.
 * I always thought that the clock roaches were there because Rose changed her own personal history 1: where she had already crystalized her own time line (important: Not just the Doctor, but her personally. The Doctor's presence both times just gave the paradox strength through redundancy) and 2: in a way that made her present changing of the timeline impossible, in 3: a universe where the Time Lords weren't around to be Clock Roaches in place of the scythe-dragons. Had the Time Lords still been around, they would have tried to make it impossible, presumably without eating everything in sight, had Rose's father disappeared instead of dying the the road then run away after she saved him or stepped out in front of the car as it was passing by later the timeline would have been Close Enough, and had Rose not been there twice, only come back once the past of that time was changed enough to have her not be there, things might have turned out differently.
 * This seems to be pretty much confirmed for the most part. The reason he hates anyone but him changing things is exactly becuase he knows what can and can't be changed, what points are "fixed" and which are "in flux". It's when someone changes what is supposed to be a "fixed" point that things go wrong, so since he knows that he's the only one that can tell, he just does his best to convince people that any meddling is bad to prevent them from changing the wrong thing. As to the clock roaches, it was out right said they only show up when an outright paradox is created that the universe/time line can't take care of on it's own. Which is why crossing your own time stream is the biggest no, no for time travelers, since that is the easiest why to create some sort of paradox.

The Doctor defends Earth so much because he has to.
Just about every human companion the Doctor has ever had has saved his life at least once. Therefore, he has to maintain the history of Earth to ensure these companions are still born at the right time and end up in the right place to meet him. Otherwise, he'll disappear in a puff of logic. And the more he defends Earth's history, the more times his life gets saved by humans, so the more he has to defend Earth's history.

As part of this strategy, he keeps a copy of the Complete Works of Shakespeare in the TARDIS, and consults it frequently. If "Troilus and Cressida" goes missing, that means the timeline is broken at some point before Vicki is due to be born, and he has to go and fix it. If the entire book disappears, Shakespeare needs rescuing.

Regenerations are a resource and can be harvested.
We know that Time Lords are given extra lives through a process not yet explained. The Master has done many things to give himself more lives. When he was given 12 more lives, this proved that the Time Lords are stingy about giving out more but will under dire circumstances. When a Time Lord kills another, it is stated that they "steal" each other's lives. They don't just hand them out every couple of years for a couple of reasons:
 * Twelve lives is an awful lot, and most Time Lords don't travel around that much.
 * A Time Lord who dies a lot is clumsy and a waste of resources.
 * Time Lords may want to die eventually. When the sixth doctor was afraid he was stranded in the Tardis, he lamented that he still had to live through his regenerations, not able to die immediately, barring suicide.
 * Romana was able to choose what she looked like. It could be some sort of luxury that rich, important or honored Time Lords can afford.

If it is a resource, it could be renewable or nonrenewable. If it's renewable, it's probably difficult to get hold of, and taking too many lives at once could damage the means of acquiring them. (Even renewable resources can get used up if misused. Passenger pigeons were once a renewable resource.)

If it's nonrenewable, then it's simply a luxury.

Romana's second regeneration suggests it's renewable.


 * Wasn't that confirmed (if not in the details) by the TV Movie?

The Doctor got the Master's lives as he died.
Well, why let them go to waste?
 * Who says he's dead? He's The Master, after all.
 * Despite  this is not necessarily Jossed.

There are no limits to a Time Lord's regenerations. The Time Lords of Gallifrey have merely been putting limits on them; without them, there are no more limitations to the Doctor's regenerations.
Ok, this may take a bit of thought, but think about it for a second.

As listed above in previous WMGs, the Time Lords can grant new regenerations to any Time Lord (as they tried to do to the Master in The Five Doctors, and presumably succeeded with the Master during the Time War), and even transfer one Time Lord's regenerations to another (as seen with the Valeyard during the Trial of a Time Lord saga). Further, the few times a limit on regenerations is mentioned, such as with Borusa in The Five Doctors, there always seems to be a lot of resentment associated with the concept of a limit on the Regenerations.

Now, consider that whenever the concept of Regeneration is brought up in the new series... there's no mention of a limit to the regenerations whatsoever. Ninth doesn't bother mentioning that he's got a limit on his regenerations, nor does the Tenth ever hint at it - not even when he redirects his regeneration into his hand during the finale of the fourth season. These events, obviously, all take place after the Time War.

The Time War where the entire planet of Gallifrey burned to a cinder, as the result of... oh, wait.


 * Tenth once said to Rose that he doesnt die: he simply regenerate. This seem to imply that he has no limit on how many times he can do it. That, or the Time Lords gave him a really long (or infinite) cycle in the Time War.
 * He says he doesn't age. Different thing.


 * No, even better: he has ALL of the regenerations of every Time Lord. Recall how when one Time Lord kills another, they get their regenerations? Now think of the conversation between Eleven and House, in The Doctor's Wife.

House: "Fear me. I've killed hundreds of Time Lords."

The Doctor: "Fear me. I killed all of them."

He destroyed Gallifrey, and in doing so killed every single one of the Time Lords. He got all of their regenerations, and will essentially live forever unless he chooses otherwise.


 * A small thing, but it does reinforce the idea that the limit on regenerations was set by the Time Lords deliberately. In The Brain of Morbius, the Doctor scolds the Sisterhood of the Sacred Fire for trying to live forever, saying without death there can be no change and progress to a society. Sounds like he's talking from an informed position, that may be the belief that caused a limit to be set in the first place.
 * Alternately, the limit on regenerations might have been imposed because Time Lords who'd lived through too many different incarnations are prone to become more and more unstable with each life. Consider how the Master has become progressively more bonkers since he exceeded the 13-life limit.

The Doctor's name is Thedoctor.
Due to a curious quirk of linguistics and language, the Gallifreyian name 'Thedoctor' sounds curiously similar to the Earth-English title 'Doctor' coupled with a definitive article. Thedoctor is quite used to it, however, and is quite happy to be addressed by the shortened 'Doctor'.
 * Curiously enough, he used "The Thedoctor" as an alias in Last Man Running, one of the Past Doctor Adventures novels. (It was an acceptable way of fitting in because the culture was prone to giving "toodies" (people from Second Planet) names like Pe Pertanor, Ri Rinandor and so on).
 * Well, in "Planet of the Dead", when asked his first name and surname he simply replied "the Doctor" to both.

Beware, following paragraph contains brain-melting Hand Wave Physics that even the Troper posting it doesn't really comprehend
In the Whoniverse, there are three dimensions of time. There's first-order time, which is what we experience and the TARDIS can move freely in. There's second-order time, the source of not only all the space inside the TARDIS, but also explains how the Racnoss Queen was able to bring the TARDIS back to the present day despite it being four and a half billion years in the past, as well as how the passengers inside the TARDIS continue aging at their normal rate rather than regressing to infancy as they move into the past; when they step into the TARDIS, they become protected from the effects travelling backwards in regular time would have, because they are standing in second-order time. Finally, the Heart of the Tardis contains third-order time, explaining its absurd power; it can disrupt the effects of the other two forms of time, making it an ultimate weapon if used properly, but its effects corrode the second-order protection on human and Time Lord cells. (Clutches head)

UPDATE: This is basically a Techno Babble explanation for San Dimas Time, but with added "Ow, my head".
 * I thought of something similar for the way time runs in the Whoniverse, with there being two dimensions of time rather than one (why not, after all, we have three dimensions in space). If you graph the two temporal dimensions on an axis, you'd see that reality runs like a diagonal line between the two, moving in one direction (lets say to the left, for this discussion). The TARDIS moves along this "line of reality" when it time travels. Hence how the TARDIS can be a "second out of sync with the rest of the universe", and how time can "run out". One can measure time based on the movement of the universe through the secondary dimension in space (what is used in the TARDIS), or one could use their position on the "line of reality", due to each X point on the line having a different Y point, to tell time.
 * Note: There is actually a real life scientific theory that time works like this.

The TARDIS is not necessarily bigger on the inside.
Surely, if the chameleon circuit worked, it would be able to appear as an object larger than its (presumably fixed-volume) interior? This also raises the question of what it looks like with the circuit switched off.
 * The TARDIS's natural form is "whatever would be least conspicuous in this situation." It has no 'real' form. Try to wrap your mind around that.
 * So what would it look like at a TARDIS convention?
 * First one to arrive would try to blend in with the venue (column, pot plant, booth with TARDIS merchandise, etc.), and the rest would then take their cue from that. Simple.
 * And what if they all arrive at the exact same time?
 * The EU states that the default appearance of a TARDIS is a grey box with a sliding door. Technically, that's not its "real" form, but that's probably what it would look like at a TARDIS convention.

Each Tardis is powered by a Chaos Emerald.
It explains the glow. Back when Time Lords weren't an endangered species, they got enough through time travel and alternate universes. The Doctor's Tardis uses a Yellow Chaos Emerald.
 * My Sonic lore's limited, but aren't there only seven chaos emeralds total? Plus, when did the Doctor's TARDIS ever have a yellow glow?

There are a race of human Time Lords somewhere.
They "regenerate" by having a copy of their Gallifreyan counterparts' memories transferred from one person to the next. Therefore, the Human!Doctor's regenerations are; Peter Cushing!Doctor, Jackson Lake, possibly Doctor!Donna, and then Hand!Doctor.

Many inconsistencies are explained by the Literary Agent Hypothesis
Many fan theories are based on slight inconsistencies somewhere in the show's long run. Some of them are just for fun--not a lot of people really think that every story takes place in the Matrix--but some of them are meant to be serious theories. While these theories do explain away the inconsistencies, they also help lead to Continuity Snarl, which isn't good. It may make more sense to interpret these as Literary Agent Hypothesis--the inconsistencies didn't happen; it's just a mistake in how the production depicts the Doctor's life. Some such theories include:
 * Season 6B
 * Any theory which tries to explain why we never saw something before the writers dreamed it up (Torchwood, the Doctor's second heart, etc.)
 * Explanations of why the Doctor gives inconsistent ages.
 * Any attempt to explain the faces in The Brain of Morbius.
 * Aww, but we like the Continuity Snarl! It's a Time Travel series -- it's not complete without one!

All the Time Lords are still alive
The first Time Lord, Omega, was hit in the face with a supernova and dropped into a black hole. He(?) survived...and built his own "antimatter" universe. The Master is a second example. There's no reason to think any of the others are easier to kill.
 * Furthermore, not only are all the Time Lords alive, but most of them, after the Time War, escaped to other realities, hence why so many characters in other works are seen as Time Lords.

Most of the Doctor's regenerations are mentally unstable.
Think about it.
 * Most? Try all. Why do you think we love him so?

Real life time travel will be used to make a team up movie with all incarnations of The Doctor

 * And it will be awesome.

Time Lords really do exist, but they're living normal lives here on planet Earth.
Consider the following.

Donna is the Doctor's Mum
The Lady from End of Time has been confirmed to be the Doctor's mother (this was in the comantary for said episode), when Wilf asks the Doctor who she was, the camera pans over to Donna. Thus we must conclude that Donna is the Doctor's mum and that the Doctor really is half human.
 * Actually, if you look closely, he's looking at both Donna and Sylvia.

A Time Lord's previous incarnations become creatures of consciousness upon "dying"/regeneration.
This could explain where  got the idea from. It would also mean none of the previous Doctors are truly gone. Hey, Ten could have stuck around in the TARDIS!
 * Nonsense. Why would they need to make the sanction to end time to begin with if they were fine after dying? Why would Rassilon defiantly claim he "Will. Not. Die."?

The Time Lords are highly evolved Britons
Why do all the Time Lords have British accents, and the Doctor focus so heavily on the human race (and prefers human companions)? Because it is from them that his own race is evolved. At some point in the future, as the people of earth spread, those from the what we call the UK settle on Galifrey, evolve somewhat, and discover time travel. They use this to go back to the beginning of time, and over the millenia they forget or conveniantly hide their origins (which the Doctor and perhaps the Master discover). The Doctor needs to save the human race in order to cause himself to exist. The Doctor (11): No. You look Time Lord. We came first.
 * Jossed:
 * That doesn't Joss it. Even if he's telling the truth, they came "first" by time traveling back to before Humans evolved before they founded Gallifreyan culture.
 * humans and time lords are EACH OTHERS originators. humans evolve into time lords and go back in time to sire the first humans, who go on to become the time lords, and so on. its a stable time loop, like kirks glasses. FERPECT.

David Cameron acts out the "It's a gas mask" scene when no-one else is around.
Just because I can see the Leader of the Opposition doing that when no-one's watching. I can see Gordon Brown imagining himself gassing the Cabinet, too.
 * This WMG even funnier now, because David Cameron has been appointed Prime Minister (bullet point written in June 2010).

The TARDIS is the star of the series
Only one thing happens at the very beginning of the show that has any real significance in the Doctor's life overall: the chameleon circuit breaking. What other reason would the story start at that point? Because it's the only constant.
 * This troper can name two very significant things from An Unearthly Child that affected the Doctor's life. Firstly, he meets the two people that make him realize just how amazing the human race really is. Secondly, he aquires the alias "the Doctor". Those are some pretty big things, and are much more important than the Chameleon Circuit breaking.

There are no such things as Time Lords.
Times Lords are just a product of the collaboration of deranged tropers
 * Which means that Crazy Eddy (or whoever it was that made this site) works for the BBC.

The Doctor uses the companions to keep track of his personal timeline.
Besides enjoying their company, the Doctor likes to travel with different companions so that he can keep track of his own timeline within the span of a regeneration. This is particularly useful if the Doctor knows he needs to initiate certain events in his future to create a Stable Time Loop, but doesn't have an exact date for when they occur. So, for example, in Blink, Sally Sparrow gives him a folder of information to use when he gets sent to 1969. Well, it would be pain to carry around a folder for years and years if, say, he weren't to get sent to 1969 until a hundred years after meeting Sally in his subjective timeline. However, since the folder contained a transcript that referred to his current companion, Martha, he would know that the event was going to occur soon-ish and that he should keep the folder with him.

Potentially the Doctor could have a whole room of stuff that he would need in order to do certain things at certain times. Using the companion system, he would just carry around whatever he needed for time loops that occurred during the tenure of a certain companion. He probably gets some info on whoever was supposed to be with him at the time (since it's likely someone he hasn't met, yet) and then files everything under certain descriptors.
 * As a bonus, perhaps the reason the Doctor travels primarily with young women is that women's fashions tend to be highly variable. The right description could point him in the direction of when a companion is from, making it even easier to narrow down their identity. Plus, if someone is dressed like a freak (for your time period) you'll notice them more and be able to give a better description.

Regeneration causes Time Lords to develop a resistance - but not an immunity - to what killed them

 * This explains how Ten was able to . But wait! you say. Ten died of   Well, yes, but perhaps it took a good deal more the second time. So Four died by falling (or rather, the sudden stop at the end), but Five onwards would have to fall from a much greater height before it killed him. Six would take longer to succumb to spectrox poisoning - or might survive it. Seven wouldn't be prone to concussion. This would be a natural self-preservation method for Time Lords, allowing them to overcome their weaknesses. (And given the terrible ways the Doctor tends to die, he's gonna end up indestructable.)
 * Would this mean that after Seven's death the Doctor is Immune to Bullets ... or to medical malpractice?
 * It's quite common for people to survive ridiculously high falls if they have something stopping them on the way down -one woman supposedly survived a parachute jump where her 'chute failed with only one or two broken bones because she hit a (single!) telephone wire on the way down. And Ten hit glass. It's not impossible to survive that fall. Depends how you land.

Time Lords have a very low tolerance for sugar.
In fact, the sugar found in a single Jelly Baby is enough to put a Time Lord on a sugar high akin to that of a human child after a full bag of Halloween candy.
 * As evidenced by Simm!Master.
 * The Fifth Doctor spending most of his first serial in a coma? Sugar crash.
 * This also explains Ten doing exactly the same thing - that tea had a load of sugar in it, I'll bet.
 * If it was that bad, he'd be on a Crazy Awesome, near-psychotic sugar high every time he ate a bana- ...You know what? This could be right.

The Doctor's TARDIS is "obsolete" exactly because of its reliance on six pilots.
The progress in TARDIS technology made it possible to increase automation and allow a single person to pilot it. This essentially obsoleted the model the Doctor ended up hijacking.

Gallifreyans eventually become humans via a temporal loop
.

There's a theory which has been around in one form or another for a long time that humans eventually evolve into timelords. Possibly, though, it may work the other way around. At some point they'll work out how their holier than thou attitudes were basically the root of their own destruction. Maybe Timelords, after their near extinction in the timewar, had to find some other way to bring their species back into existence: they knew that the only way they could do this would be if they came back without the hyper evolved abilities that they believed made them superior to other species - their time senses, etc. That "ascension" thing that was going on about in The End of Time part 2 might be adaptable so that it's less an ascension and more of a simple change. The Doctor will probably be involved in this in some way, probably during his last incarnation or something dramatic like that. Nothing like helping your own extremely arrogant, over-supremiscist race turn into your favourite species. (Of course, we humans have quite a bit of arrogance and superiority in our make up ourselves - maybe that came from the part of us that used to be Timelord. Heck, you can take the man out of the timelord but you can't take the timelord out of the man.)

Via some kind of weird highly advanced science applied to the timeline at the end of the universe, the Timelord DNA will be split, from a triple strand, to a simplified double helix, and inserted into the the early days of planet earth: Humans and Timelord will evolve and develop, together in the same universe during the same timeline, utterly unaware that one is a future version of the other - ironically, the humans are, chronologically at least, more advanced than timelords.

Alternatively, humans are the distant ancestors of the Time Lords.
They're descended from humans who managed to survive the end of the universe, by fleeing into the distant past. Determined to survive at any costs, they spent eons making sure time could not kill them. This was done by becoming the masters of time, aka Time Lords. At this point, however, the Time Lords have completely forgotten of their human origin. This is why humans are indomitable: they have to be, since their entire existence is one big Stable Time Loop. Not to mention how screwed up the timeline would become. And this is why the Doctor has such hefty Plot Armor-he is the crux, preventing it from all collapsing inwards.
 * Given that we now know that you can get a (near) Time Lord by exposing a human fetus to the Time Vortex radiation . ..
 * Surprisingly more possible than one thinks. Assume the whole Neutrinos-faster-than-light thing pans out, opening the door to time travel in some way. That explains the time-travel aspect. Now add in the astounding rate at which humanity is advancing medical technology, including regrowing limbs. Regenerations, if given enough advance. And finally, a good old fashioned wormhole generator, or something of that sort, to bring Humans across the stars... to Gallifrey, billions of years in the past. Now, add back on those few billions of years advancing in technology, (and the eventual chaos that woud bring) alongside the invention of the TARDIS (All of humanity's achievements into one convienient device) and finally remove their "humanity" with liberal doses of erased and forgotten history, alongside egos the size of planets. That is Gallifrey, the Time Lords, and in it's own special way why the Doctor and so many other beings are so damn interested in little ol' Earth. Time Lords are like humans? Humans are like Time Lords? No... Time Lords are humans.
 * Stable time loop? Too easy. How about a stable OSCILLATING META TIME LOOP!? Humans are the precursors of the Time Lords but only on the final iteration of the timeline in which Time Lords were wiped away from history by the Time War. Once set up, the Time Lords use an awesomely powerful paradox machine to protect themselves from enemies that would try to wipe them out through their weaker human ancestors and deliberately change the course of human history to disguise their origins. They do this so well they eventually forget about their true origins themselves. Eventually, of course, the Time War occurs... wiping every Time Lord (barring the exceptions) from history and getting the ball rolling again. And, yes, the Doctor is "the Other". (River, on the other hand, may well be the Time Lord answer to Eve)

The Time Lords evolved from Trills.
When the host body grows weak, or is injured, they simply change to a new one. The new form remembers its previous lives, but is still a different person in the long run. There are some key differences, but technology, and millenia of evolution solves that problem. Makes sense, doesn't it?
 * Aren't Trills symbiotic lifeforms?

The Doctor is Jesus in Purgatory.
This is pretty much what TV Tropes is trying to tell us.

The Master is Satan in Purgatory.
As a guest, not the host, since the Doctor is Jesus. This is pretty much what the end of the  series is trying to tell us.

The Dalek Eternal is responsible for keeping the purity of the Daleks
Episode 3 of Eleven's first series introduces five Dalek castes, one of which is named the Eternal. The rest have obvious roles, but not this. However, none of the others seem to deal with the whole race-purity thing- so maybe the Eternal is a historian and Inquisitor-type, who ensures that they don't change- they stay eternally pure.
 * Daleks have always reminded me a little of white blood cells. In which case the Eternal would be like a memory B-cell, who’s role is to live a really long time and reproduce when need be.

The reason the Doctor’s personality changes post-regeneration is a protective adaptation.
His personality changes to alter whatever behaviors either caused him a lot of trouble or led to his ‘death’. Justifications are as follows:
 * The First Doctor was secretive and crotchety, this led to his contrasting friendly and playfulness as the Second.
 * The Second was too disorganized and that led to him painting himself into a corner (metaphorically speaking) in “The War Games”. Despite this being a forced regeneration, his serious and orderly Third self resulted from that.
 * The Third Doctor’s reliance on order and rationality got him into trouble a lot, thus the manic nature of his Fourth self.
 * The Fourth Doctor’s huge ego gets him killed, so he regenerates into the more mild-mannered Fifth.
 * The Fifth Doctor is too heroically noble and ends up dying because of that, thus the more ruthless and violent Six. Also explains why Six strangled Peri, it was his subconscious viciousness blaming her for the death of Five before he realized what he was doing and stopped.
 * Six was too much of an ass, so Seven started out more fun-loving and cheerful.
 * Seven ended up being way too thoughtful and relied too heavily on observing and planning to look outside his TARDIS before stepping right out into a gunfight. Eight became more reactionary as a result.
 * Eight was not a soldier by any means, that’s why Nine became a lot more a loner survivor.
 * Nine’s loner nature and death wish caused him to leave Rose behind and him trapped on Satellite 3, directly causing both his forced regeneration upon absorbing the time energy, and his more friendly charismatic personality as Ten.
 * It’s too soon to judge Ten to Eleven, but they seem similar in personality so far, so perhaps it was just an adaptation against the “Time Lord Victorious” he was becoming, and his immediate welcoming of Amy Pond into the fold supports the fact that the loner nature he re-developed as Ten was one of the major personality flaws he faced shortly before death as well.
 * Eleven seems generally more detached and both overtly and subtly (gestures etc) more alien than Ten. This could be a reaction to Ten's very companionable nature - Eleven has become a little more distant to prevent him becoming as personally invested as Ten, while also protecting him from the severe heartache Ten suffered whenever his companions were taken from him.

Time Lords are born with Caffeine in their blood
That's why so many of them are so hyperactive.

The Doctor is the eighth Endless
He's really old, his regenerations are very similar to Dream's death and "replacement", and his "name" does begin with a "D".

Regenerations are powered by sacrificing lives.
In a cross between Planescape Torment and the resurrection gloves from Torchwood, regenerations are actually powered by sacrificing the lives of random strangers across the universe. The 13 regeneration limit was imposed by the Time Lords to limit the sacrifices made in their name, and the mechanism is a limit on the number of time-energy bridges between the sacrificed person and the receiving Time Lord. Naturally it's a secret closely guarded by the Time Lords, but it's one the Doctor will have to face when he reaches his thirteenth regeneration and realises that he can continue living, but at a cost...

The Time Lords are really .
The Doctor's appearance is, among other things, a disguise so his human companions won't be disgusted beyond belief at his true form. The various regenerations are actually updates to the Time Lord's holographic disguise. In some ways, this can explain why he gets younger with each transformation: with each update, the Doctor becomes a face that the current generation can trust enough to time-travel with.
 * Starfish Alien is childs play. Time Lords are cosmic horrors.

The Doctor subconsciously manipulates time
Or more accurately, probabilities. I don't care how brilliant he is, he's been in plenty of situations where that shouldn't have been able to help him. Faced against impossible odds, so often it seems the fates simply align for him at the last second. Perhaps it's because, as a Time Lord, with his vague temporal awareness and attunement to psychic energy, he is constantly twisting reality toward the desired outcome, applying a psychic force on time. Basically, the 1 in a million chance becomes the 1 in 100 chance because of the Doctor's mere presence. This accounts for at least some of his enormous success rate. This also explains what River said about the man the Doctor will eventually become, able to send entire armies fleeing with relative ease. His ability to manipulate the outcome will improve as he becomes more aware of his powers, which also manifests in things like snapping to open the door of the TARDIS.
 * And yes, I do realize much of his success can out-of-universe be explained via Plot Armor and by being the main character. But in-universe, I think psychic projection makes sense.
 * You'll love this: one of the Eighth Doctor audio adventures hinges on the existence of Time Lord technology that does exactly this, so it has a precedent in Time Lord society.

The canon of the Time War is time-locked
It's not just in-universe: the reason we've seen so few expanded universe works dealing with the Time War is that its events are as inaccessible to the writers as they are to the characters. This is why we haven't been able to 'travel' to the Eighth Doctor's regeneration into the Ninth. Our understanding of the Time War is exactly the same as that of most species in the universe: we know it happened, we could name some events and participants, but we're unable to observe it directly to any significant degree.
 * You do realise that is bad news for us all...

Everything is canon
Everything that's in every single episode, novel, comic, audio and even the film is canon. Including the Curse of Fatal Death. As characters like the the Time Lords and the Time Agency move throughout time, they're forever changing the course of history. This could be small things like changing when the Doctor first met the Daleks to how Time Lords reproduce. A Us are canon in the Whoniverse, so even if something isn't canon in whichever Dr Who work you're currently enjoying, it is canon somewhere else. ''“Y’know, the thing is, Amy, everyone’s memory is a mess: life is a mess. Everyone’s got memories of a holiday they couldn’t have ‘bin on, or a party they never went to, or met someone for the first time and felt like they’ve known them all their lives. Time is being rewritten, all around us, every day. People think their memories are bad… but their memories are fine. The past is really like that.”'' In short, there's no reason not to think that the Doctor doesn't remember being loomed, being half-human and also being born to two Time Lord parents... even if the last is that which he acknowledges as his "canon" history. Until even that's rewritten.
 * Though this does make it even harder to figure out what's canon right now. All we can know is that what we're currently experiencing is canon. That exact moment. Everything else is in flux.
 * Seems to have been confirmed by the "Nights" shorts from the Season 6 set:

The Doctor is one of the Endless
He is the anthropermophic personifercation of Deus Ex Machina. After all he is a god in a machine.

The last regeneration of a timelord is their last because they hit a negative "age"
The Doctor gets younger with every regeneration, starting from the very old first Doctor and all the way down to the youngest actor yet. Additional regenerations can be "acquired" by aging naturally (or having an accelerated aging effect).
 * If this is true, then the events of "The Leisure Hive" and "The Sound of Drums/Last of the Time Lords" mean the Doctor is set for quite a long time.

The Doctor and the Tardis got married some time during the series.
It's possible.
 * Seeing as a human has turned into a TARDIS, I suppose the reverse is not out of the question
 * One of the episode titles describes the TARDIS as "the doctor's wife"

The Dream Lord is the Start of Darkness for the Valeyard
An incarnation of the Doctor, made up of all the evil that is within him, right between his eleventh and twelth regenerations? Sounds like an almost textbook definition of the Valeyard to me. Especially with The Stinger in the end of the episode that shows the Dream Lord is not quite gone...

There's a Time Lord named "The Batchelor" and he's an epic fail.
In the UK (dunno about other countries), the three levels of univerity degrees you can attain are "Batchelor", which is the basic university-level qualification; "Master", which is a higher qualification and 'Doctorate', the highest degree level that gives you the title of "Doctor".

Anyway, to actually get to the point, the Doctor is (arguably) the most awesome character in the show, beating baddies and generally winning stuff. The Master is much less successful, usually being absolutely humiliated on the brink of victory. One thing I've learned through watching Doctor Who is that a coincidence is NEVER just a coincidence. No matter what. Therefore, there is another Time Lord around somewhere, named The Batchelor. And he is not only Genre Blind, but also made of Epic Fail.


 * Or he just goes around as a pimp, like the Doctor and The Master's theme. (The Doctor fixes stuff. The Master tries to take over the world.)

The Batchelor is the reason why the Doctor always has to fix history.
Wherever Batchelor goes, because of his Fail he will end up setting history out of the original flow. Like "Voyage of the Damned". Batchelor brought the owner of Titanic to the idea of crashing the cruiser. Or prior to "Alien of London" he inspired them to their buisnessplan of destroying Earth.
 * The show inverted this trope in "Fires of Pompeii" as the Doctor ruined everything.

The inconsistencies with The Doctor's Age are due to his lying about his age out of vanity.
This would be the easiest explanation as to why he claims to be just over 900 as the New Series starts, but was 953 during Time and the Rani.
 * It would be in character too, as he was called out over lying about his age by Romana in The Ribos Operation.
 * A thousand years is the Time Lord equivalent of thirty for humans - he wants to stave off the dreaded fourth digit as long as possible, and instead keeps counting the early nine hundreds over and over.

The inconsistencies with The Doctor's Age are due to his changing how he keeps track of his age.
Astronomically speaking, a year on one planet is highly unlikely to be the same length as a year on another planet, since one year is the length of time it take a planet to complete an orbit around its' star. Given that, there are a few possibilities of how The Doctor might keep track of his age.

1) Earth Years 2) Gallifreyian Years 3) Intergalactic Standard Years (assuming all the civilized planets have an agreed upon standard as to what constitutes a year)


 * It's not only possible but highly likely that The Doctor may have converted his age from the Gallifreyian standard to Earth years for the ease of reference of his companions early on and then - with Gallifrey dead - gone on (in the New Series) to use the Gallifreyian year in charting his age. This assumes that Gallifrey has shorter years than Earth.
 * A shorter Gallifreyian year would also explain why The Third Doctor said he had been a scientist for several thousand years, but then gave his age as 748.


 * Alternatively, maybe he used Earth years to start with (he was rebelling against Gallifrey and it's laws for a fair bit during the Classic series, wasn't he?) and because Gallifrey got destroyed, he decided to remember his planet through little things- like using the Gallifreyan calendar. This would work if Gallifreyan years were longer than Earth years.

The Doctor's name is Sweetie.
Self-explanatory if you're familiar with River Song.
 * Jossed. The name whispered in his ear in "Forest of the Dead" and "Sweetie" are obviously two different things.

Alternatively... The Doctor's name is Jelly Baby.
The Fourth's obsession with the little candies stems from the fact that they share the same name and was also him suggesting, subtly, that the people he offers the little candies to that they need a little bit of him, in both ways that could be taken. Flash forward to when the Doctor tells River Song his name, she finds it hilarious that he has the same name as a candy and starts to call him sweetie because of it. Jump back to River Song revealing that she knows his name and Ten mentioning there is only one reason he would reveal his name, it is because he is embarrassed by his name and doesn't want people to know that he has the same name as a candy.
 * Dude, you deserve a Made of Win for making my day.
 * His name is Sweetie Jelly Baby.

The series (especially later episodes) is an AU of Peter Pan.
To start off, we have the title character who never grows up (technically, the Doctor ages but incredibly slowly; and regenerates into a younger form every time he dies, effectively gaining immortality). Even the Fourth Doctor has said that there's no point in growing up if you can't be childish sometimes.

Before the story begins, the main character runs away from home and meets a magical creature (the TARDIS could be compared with Tinkerbell) who gives him the ability to "fly," or travel through time and space. Occasionally they pick up a few hitchhikers (Lost Boys/companions) and have wild, fantastical adventures while thwarting the evil schemes of the murderous army (pirates/Daleks) and their ruthless, handicapped leader (Hook/Davros).

The Doctor is making a conscious effort to appear younger.
He's starting to feel the weight of hundreds of years and wants to be youthful again, in a midlife crisis sort of way. This contrasts with Ten's mention of his early incarnations "trying to be old and important, like you do when you're young" in "Time Crash." All Time Lords have the power to will themselves to be younger during regeneration (see The Master), but the (chronologically) older ones, like  have again decided that they need to be "old and important," or perhaps have not regenerated in a long time.

The Eighth Doctor died at the hands of a massive meth overdose...
...inflicted by The Black Glove. (I wasn't sure which of those things to put after the other.) Anyway, I got this idea after noting that while the Doctor has always been eccentric and lively to certain degrees, the last three in particular have been increasingly ooh-what's-that energetic. Now rather than being, say, the result of rising standards in the media of what can hold our attention as a quirky, quick-thinking hero, or something to that effect, a friend of mine (not too up on Doctor Who) suggested offhandedly that he had discovered meth. Now, of course, our friend the Doctor would never turn to drugs like that, but what of a sinister organization known for weaponizing drugs and using them to push the boundaries of succeeding at killing the hero? Well, that it should be the villains of a comic I've never read is strangely-fitting icing on the cake, but the point is he died of too many uppers and is still working through it.
 * If River Song truly is the Doctor's future wife, she will obviously also be Susan's Grandmother.
 * Jossed, given the whole time lock thing and the Tenth Doctor not recognising River.
 * If Susan does indeed return to the show (it could happen!), it will be a regeneration. Last I heard, Carole Ann Ford (who originally played Susan for those who haven't read the Character Sheet yet) hasn't been in the best of health.
 * River Song has met the other Doctors, we just haven't seen those encounters. That's how she knows so much about the Doctor.
 * Jossed. The Tenth Doctor has no idea who she is. She recognises the faces because she's been collecting images.

The Doctor is a Charm Person
Think about it. People who have just met him begin to trust him with their lives despite the fact he is very, very odd. He often talks his way out of dangerous situations easily. Amy Pond also should not trust the Doctor the way she seems to at times in the Beast Below. And Rory filps from "You make people a danger to themselves!" to "We can't just leave you!" in half an hour. He could easily be giving off some low level telepathic signal that encourages people to believe and trust in him.

The Doctor absorbed the Master's personality
upon the latter's death in The End of Time. This is why his regeneration was so destructive: the Master was fighting to get out, or at least take over the body, and this inner struggle was projected onto the TARDIS, causing it to need to regenerate as well (alternatively, see below). The Dream Lord was a hybrid personality composed of both the Doctor and the Master, and will become the Valeyard.
 * Not really made evident anywhere. Care to expand on what Master personality traits are there?

The TARDIS is...
a Time Lord. Wait, don't hit me, at least let me explain! The TARDIS is a biological machine grown by the Gallifreyans, correct? Now, what if the title of "Time Lord" is not a name for their race, but instead for any being with a heightened consciousness and time senses? Gallifrey has an effect on beings born on it, which is why the Gallifreyans are Time Lords; this effect also causes their biotech to become Time Lords, as well. When the TARDIS' interior was destroyed during Ten's regeneration, that was actually because the TARDIS was regenerating at the exact same time. This also explains why the TARDIS looks different at the start of the new series (it does, doesn't it? I haven't seen classic Doctor Who): it regenerated.

The Doctor regenerates because of Mushi
The golden sparks coughed out by the newly "cooking" Doctor are very similar to the spores coughed out by those effected by some forms of Mushi (Obscure and ludicrous but just crazy enough to be considered).

River Song is the Master
It would explain a lot. We've never proven Time Lords can't regenerate into a different gender...
 * Wasn't there an episode of the Old Series where a female regeneration of the Doctor appears? See, totally possible!
 * You're thinking of the comic relief episode for Red Nose day.
 * Jossed. She's

Sometime during 11 or 12's run, we will have "The Four Doctors" special.
If I Recall correctly, there have been Two, Three, and Five Doctor episodes, but not Four. It will include his Ninth through Eleventh incarnations. The last one will either be Eighth (during Eleventh's run) or Twelfth (during his own run).
 * That would be an awesome story for the 50th anniversary in 2013. They could maybe get 4th through 7th back in some form. Davison and McCoy would be capable of doing it at least...
 * Slightly less likely to due a new Audio Adventure Special being titled The Four Doctors. Not that they haven't reused titles for completely different stories, End of Time, or remade the stories into a new version, The Lodger, or something completely new.

River Song is Miss Frizzle
See?
 * And if River Song/Miss Frizzle is a Time Lord, then that means the Magic School Bus is a TARDIS. Makes sense to me.

The Doctor likes the letter R.
Romana, Rose, River... He likes those R-named girls. That's why he didn't go after Martha or Amy or Jack. Their names didn't begin with R... Rory might be in trouble, though.
 * Don't forget Reinette.

The Doctor's more questionable actions have a reason
They're to prevent The Valeyard from becoming TOO powerful, or maybe even trying to keep him from existing. Obviously this failed/will fail/ fails.

There will be no Valeyard
He appeared in one story and hasn't even been hinted at since. By Doctor Who standards, that makes him a reasonably minor villain. Plus, there's very little to do with him. The Doctor has his dark could-be selves in the Master and the Dream Lord. Writing-wise all the Valeyard's bases have been thoroughly covered, and using him would be redundant.
 * As good as a counter point to the Doctor the Master is, there's a difference between "childhood friend gone evil" and "you yourself are destined to go evil". As for the Dream Lord, what is he other than an earlier non-manifest version of the Valeyard? Personally, I like the idea of the Valeyard being an internal war more than an external character. The Doctor struggling with his own inner darkness has been a theme of much of the new series, and I think it catches people's imagination because of the personal nature of this struggle to the protagonist. The Doctor can fight any enemy he can confront...but if the Valeyard/Dream Lord/Time Lord Victorious exists to confront like any other enemy, it's already too late because the Doctor no longer exists. Your Milage May Vary, of course, but I think an angle like this has a lot of potential to explore.

After the Doctor's final regeneration, there will still be a Time Lord running around.
Because Donna Noble will regenerate after her death and become a Time Lord.

"Hlynia" is Menopteran for "Donna".
It is known that Humanity made contact with the Isop Galaxy at some point, and Donna was one of the most famous people in the history of the universe. It is also known that the Menoptera distort Human names.

Memories and Multi-Doctor Stories: An Explanitory Theory
Every time the Doctor meets himself, his later selves don't remember the adventure from the perspective of their past selves. This is not simply to serve the story, nor is it because they're acting out what they saw their future (now current) selves do (that only happens in the event of a 'Time Crash', which I'll expand upon momentarily). It is instead because they won't remember the adventure from any perspective until the latest temporal incarnation has experienced it. This is one of the things the Time Lords regulate when bending the First Law of Time. For example, in "The Five Doctors", logically Two, Three, and Five should know that Borusa's behind the whole thing and as such prevent the Castellan's death, at the very least. Instead, they don't realize what's going on until after Five has discovered the treachery. Nor do Two or Three know what solution One is going to come up with for Rassilon's riddle because they haven't heard their past self say it yet. Why is this the case? To prevent paradoxes and protect the universe from shorting itself out, of course! (See "Father's Day" for more details on what would happen otherwise.) As for how the memories work when there's no one regulating them, we need look no further than the poor old Brigadier's misadventure in "Mawdryn Undead". His 1983 self doesn't remember at first, mostly because he shorted out part of his brain when his 1977 self touched his 1983 self (though his 1983 self hasn't been touched by his 1977 self yet), but upon re-meeting the Doctor, he starts to get vague memories as well as a discomfort with facing knowledge of his own future. Would Time Lords be more or less susceptible to this? I'd wager 'more' since they are more aware of the shape of Time itself. Now, while we're discussing the Brig's own personal paradox, I think we should look into the Blinovich Limitation Effect. This is the discharge of temporal energy that occurs in an uncontrolled meeting between a person and themself from a different point in their own timeline. It has been theorised (and demonstrated in "Father's Day") that such a discharge would be catastrophic. This brings up the question of why the Brig didn't destroy the universe when he touched his temporal double. The fact is that had it not been for the mutants' machine being prepared to siphon off a large amount of temporal energy already, the blast would've been far more catastrophic. This is a digression from the main point, however. As for the companions in such scenarios, I suspect their memories are purposely clouded as well. This isn't an issue in "The Three Doctors" or "The Five Doctors" since Jo was traveling with the latest Doctor in the former, and all companions were taken out of time concurrent to Five's timeline in the latter (aside from Ramona, but she was stuck in the time vortex, so that's a moot point for her). In the case of Rich Morris's brilliant fan comic "The Ten Doctors", however, things are a bit stickier as nearly every companion comes from a time before Ten's part in the timeline, so were they to remember, they'd discuss the adventure with their Doctor and he'd act to prevent many of his own future selves' mistakes next time around causing a universe-destroying paradox. Therefore, until further evidence is shown, I'll assume that companions' minds are clouded from the memories until after the latest Doctor at the time of the story has passed it in their timelines.

Now, a Time Crash (as seen in the mini-episode of the same name) is an uncontrolled meeting and as such, the memories are left unaffected since they are required to create a closed paradox. The result of a Time Crash is that knowledge is created spontaneously as you need to witness your future self knowing what to do in order to know what to do when you become them. While this results in a shorter, more intelligently managed situation, it increases the risk of catastrophe since Time has cracked and your meeting with yourself is the result. If you don't solve the problem and repair the crack very quickly, Time will shatter. The Time Lords struggle to prevent such occurances, which is why none happen until Ten's timeline after they've been Time-Locked. As for Five, he's only there because Ten remembers being there when he was him.

There is no natural limit to how often a Time Lord can regenerate.
There is nothing naturally stopping a Time Lord from regenerating more then 13 times, that limit was placed on them by themseleves somehow. Either Time Lord society as a whole, or the rulling council impossed a limit on regenerations, the reasons for this could be any, or any combination of several, ranging from population controll, averting Who Wants to Live Forever, limiting overly rediculous behaviour, making Time Lords a bit more sympathetic to non-immortals, even just straight up so they can better control other Time Lords by removing/extending there regenerations left. This explains how they would be able to grant The Doctor's remaing regnerations to the Valeyard, grant The Master new ones during the Time War. All it would take is for them to alter whatever machanic they put in place to limit regenerations in the first place. Now that the rest of the Time Lords are gone The Doctor either is no longer under this limitation (even if he doesn't know it), or will find a way to remove it prior to what he things will be his final death.

Steven Moffat needs to watch Marble Hornets.
And give us a Crossover. Because Slender Man vs. the Doctor would be awesome. Original poster here, with an updated variant:
 * It would also be even more terrifying than Blink
 * Perhaps the Slender Man was the one behind the TARDIS's destruction. That's right. That's him saying "SILENCE WILL FALL". When he's faced with The Doctor he doesn't screw around.
 * Uhh...uhhh...guys? You know the series 6 trailer? Did you see that thing at the end?
 * Oh god. Oh god oh god oh god oh god oh god!
 * I think that's one of The Greys, but yeah, I actually had the exact same reaction when I first saw it.
 * No, it's the Silence. and it's even WORSE than the Slender Man.

Slender Man is one (or a few) of the Silence
Related to the above, but taken a step further. At the end of the second part, the Doctor splices shots of one of the Silence into the moon landing footage, shots of it saying "You should kill us on sight." Humanity proceeds to kill them, but some survive. These survivors are the Slender Man. This explains why he/it/they kill people (revenge), how there's one in Iraq (Just Another Fool) while apparently silmultaneously at least two in the US. For every Slender Man blog out there, the people writing it have their own Silence following them around, waiting to kill them or drive them mad with something they can't quite explain.

The being locked inside the Pandorica... is the Doctor
Most likely a future incarnation (perhaps the Valeyard?). It's stated to be "The most feared being in the cosmos", and honestly, what else can you think of that would cause Daleks, Cybermen, Sycorax and a bajillion other evil races to unite against? Obviously, defeating it somehow involves blowing up evil future Doctor's TARDIS which results in the Big Bang that led to the Time Cracks. Status:
 * This was Jossed very quickly after being introduced.

The Doctor is a Time Lord!

 * ... Nah, thats way too far fetched.

The Doctor's final regeneration will be ginger.

 * ... And female.
 * Holy $#!+, Amy is the Doctor!
 * Jossed in too many ways. Even taking into account chameleon arch theories.

Ostriches really did have fifty-foot wingspans and fire breath.
Or rather, they will in the future- what, you think the ostrich is going to go on for billions of years without any evolutionary changes and/or humans fiddling with genetics?

The Doctor has never lied about his age
He has, however, defined it in terms of the years of planets with increasingly long orbits.

The Dalek language is syllabic.
Like Japanese, basically. Explains their MAN. NER. OF. SPEA. KING.
 * EX-PLAIN! EX-PLAIN!
 * Japanese isn't any more syllabic than English. You may be thinking of Chinese, where every individual word is a monosyllable.

The Doctor was never called "The Doctor" until the first episode.
Watch the first episode. At no point does he or his granddaughter Susan ever say that he's the Doctor. At first, Ian and Barbara call him Doctor Foreman with him replying "Eh? Doctor who?" which leads them to start calling him "The Doctor". Once that happened, The Doctor figured he'd just go along with it since he liked it.

Things like the Valeyard are exactly why the Time Lords enforced regeneration limits in the first place.
They noticed that after a certain amount of regenerations (13), they started getting crazy/evil "side effects." The higher-ups figured out the maximum amount of regenerations an average Time Lord can have without completely losing it (12) and put in place whatever technology stops regenerations after the 12th time so that they can't regenerate a 13th time. The problem is that they figured the average, which of course would not be true for every single Time Lord- some might get their evil self sooner (like after the 12th instead).

The Doctor was not one of the ones who "ran away"
When he looked into the Untempered Schism, he was one of the "inspired" but just happened to also run away, so he believes himself to fit into the latter group.

Romana prefers "Fred" for a reason.
When Romanadvoratrelundar chooses "Fred" over "Romana", could it be due to "Fred" resembling the "vorat" part?

The TARDIS name
Susan claims that she invented the name Time And Relative Dimensions In Space in the very first episode of the classic series. However, it is referred to as such numerous times by older time lords, and presumably, they wouldn't use a name made up from english words, since they speak gallifreyan. The explanation is simple : prior to the Doctor's first visit to earth, such thing as a time and space travelling machine was unheard of and thus didn't have a name in english. The TARDIS picked up the name Susan invented and updated the dictionary database used by the translation software.

But, why did Susan had to come up with a name ? The way she says it suggest she didn't make it up on the spot when Barbara asked about it. The answer is, she was probably trying to make friends with her classmates, showed the TARDIS to some of them and therefore had to come up with a name (and they ran away in fright and utter disbelief, possibly even scared away on purpose by that cranky old man).

Presumably, the gallifreyan name is not translatable, too long and pompous, not indicative enough, or alternatively, means the exact same thing in gallifreyan and all she did was translate it and give it a catchy acronym.
 * Maybe he traveled back to the time when Gallifreyans were first working on Time Travel technology, and when they are thinking of a good name he suggests the name he has always been using.

Perhaps Susan won a contast to rename the TARDIS because it was originally short for Time As Rassilon's Domainion In Space and they finally decided. Ok guys Rassilon has way to many things named after him. They then spend a few millenia shortening it to TARDIS before Susan wins the contest because she had the only entry that kept the abreviated name which the TARDIS's refused to change.

Time lords experience time backwards, the Tardis allows them to experience time forward like the rest of the universe.
The time lords experience their lives backwards.
 * Each incarnation of the doctor is younger than the previous one.
 * The Time Lords cannot do anything to stop the Time War
 * The Doctor was originally exiled for SOMETHING.
 * The Time Lords knew the Doctor was going to cause the Time War and exiled him so he could get his punishment.
 * He knows when history goes wrong for Earth.

The regeneration of Tenth Doctor into Eleventh Doctor was especially violent because Ten was holding it in for so long
Self explanatory. He's never held it in for that long before, and he's never blown the TARDIS up with his regeneration producing long streams of fire before, so the two facts are probably related. Presumably holding a regeneration in like that causes the regeneration energy to build up the whole time you hold it in, so when it is unleashed, its more energetic proportional to how long it is held in.

If the Doctor's real name is ever revealed...
...it's going to be Hu. Admit it, it will be hilarious.
 * You just had to spell it that way, didn't you? Ladies and gentlemen, the thirteenth Doctor: Shii Ann Hu. (Kaitlyn's too sane.)
 * Alternatively it could be "Hugh"...
 * You win. Forever. Although maybe his true name is Dock T Hugh.

River Song WILL kill Eleven.
What if she DOES kill Eleven, but it’s a Dumbledore/Snape thing? In order to save [insert people here], he has to regenerate. If he’s totally alone with her, and so that things happen the way that they need to, he tells her his name so that Ten will know to trust her. That gives her time beforehand to gallivant around with him, learn about the TARDIS’ brakes, gain possession of his screwdriver, “kill” him… and she could just be flirting with him the whole time simply because she wants him, not because she's his wife.
 * Jossed, confirmed.

River Song is actually the final incarnation of either Iris Widlthyme or Romana.
I personally find the idea of Iris having her poor TARDIS battered beyond repair by the Last Great Time War and having to learn to live like a normal human without copious amounts of vodka rather hilarious, but I'll settle for her being actually Romana, knowing about TARDISes and the screwdriver tech full well enough in either case. The whole "killing the best man I ever knew" is going to be a convoluted mess, very likely involving a last hope for averting the fate of the Time Lords.
 * Jossed, she's the partial Time Lord daughter of Amy and Rory.

The Doctor is the reason why deadlock seals exist.
Every single civilization in the universe that ever independently invented the deadlock seal did so with a shared goal: keeping a weird bloke with a blue box out of something.

The Doctor is really a Ctan in disguise.
He's the Deceiver. The TARDIS is his personal vessel. He's facilitating the Pariah breeding program.

Humans fall into the Doctor's Uncanny Valley.
We all know that the Doctor is (mostly) completely non-sexual, despite humans looking identical to Time Lords. This is because Time Lords have certain additional "psychic attributes" which are responsible for attracting mates, which humans completely lack (like how color and pattern is used to attract mates in some animals). So the Doctor possibly sees humans as slightly creepy Time Lord imitations. Maybe fun to adventure with but plain Squicky to do anything else with.
 * No we don't. Nothing ever states that he's non-sexual. He's romanced at least three humans, and considered "trying again" with Nurse Redfern when he returned to being Time Lord.

The Doctor is responsible for the "something old, something new, something borrowed, something blue" wedding meme
Not intentionally, mind, the meme is just the result of someone remembering and writing down a piece of his usual rambling when he arrived at a wedding several hundred years ago in the TARDIS. It came in handy later, but was just an accident at the time.
 * Maybe confirmed in The Big Bang, where he plants this idea in young Amy's mind and she recites it in order to bring back the doctor during her wedding.
 * Not neccesarily; the meme existed long before Amy. If he started it, he did it long before he ever planted it in miss Pond's mind. Er, long ago from the perspective of Earth's timeline.

The Valeyard is the result of another hand!Doctor incident in the future.
This one is accidental, like regeneration entry leaking into a nail clipping. He has no one like Rose to guide him onto the right track, and he is not happy about his human lifespan and wants to take it out on the privileged bastard, timey-wimey paradox be damned. Whatever got him through the Time Lock couldn't have helped matters, either.

The Doctor is the origin of every Healer-Priest religion in the universe
Imagine it: you are somewhat primitive cave-dwellers. A monster comes. But some weird bloke shows up too, and saves your tribe from it. His name in your language translates to "The Healer" or "The Medicine Man", because 'doctor' is really a fairly modern term. He is your savior, and then he vanishes into the Heavens. Voila! Instant religion.
 * Doctor comes from the latin word docere (to teach). Doctor is someone "who has been taught" thus a scolar.
 * Something similar is confirmed in Demons Run: The word "doctor" for healer and wise man is shared by many languages and many cultures, and comes from him.

The TARDIS is not sentient
Imagine you're The Doctor. You ran way from your home planet when you were young. You have been alone for centuries, have only had the company of some members of another species who only have a fraction of your life span and your IQ; later you kill your entire species. Sooner or later you're going to try to find companionship with this thing that has been there all your life and has defined you for centuries; this is why he talks more about it being alive as the series goes on. Like the football in Cast Away.
 * The heart of The TARDIS is just a complex power source.
 * Jossed in The Doctor's Wife where the 'soul' of the TARDIS is placed in the body of a woman. While able to speak she reveals that 'she' was the one who stole the Doctor, that the reason she's so 'unreliable' is because she always takes him where he needs to go and that she likes it when he calls her 'Sexy' and 'Old Girl'.

River is going to kill... Rory

 * Geez Rory just can't stay alive can you?
 * Umm, yes, he can. Do you mean "stay dead"?

The Doctor is, wants to be or will become/pose as a vampire
And, taken with the revelations from The Pandorica Opens (or for that matter, Amy's Choice and anything involving the Valeyard), this puts a whole new level of Foreshadowing on his musings from The Vampires Of Venice: "What could be so terrible that it doesn't mind being mistaken for a vampire?" The Oncoming Storm, possibly?
 * Specifically a strigoi. Pay close attention to the 1st sentence of the 4th paragraph: "According to Romanian mythology a strigoi has red hair, blue eyes and two hearts". Puts a slightly sinister spin on him always wanting to be ginger, no? Especially considering that Regeneration is a very neat Time Lord trick to come Back From the Dead, looking different.

The Doctor gets younger at each regeneration because he's dying with more and more pent-up life force.
His first incarnation lived hundreds of years, didn't it? His further incarnations might well have lived hundreds or thousands, but they each died after only a few years each. The leftover goes into rejuvenating him so that, barring feats of derring-do, he'll live almost as long total as he might have otherwise.
 * The Doctor has lived for hundreds of years between travels. There were at least 200 years between 4 and 7
 * It's also impossible to gauge the ammount of time he spent with Romana since they are both Time Lords.

Regenerating is part of Timelord Puberty
Timelords are born and during their first generation age similarly to, though at a much slower rate than, humans. Hence the young Doctor and Master shown in The Sound of Drums. Upon reaching a certain age they start regenerating, on a cycle or whenever injured. Each regeneration tends to be younger in appearance and more libidinous than the last, though not as an absolute rule. After 13 regenerations a Timelord has reached sexual maturity, and will continue to age at the "normal" rate but will not regenerate again. Of course this all takes so long and it's so hard to get enough mature Timelords in one area at a time to effectively propagate the species that a bunch of first generation Timelords, not seeing the point, said "Screw it, (or not) we're gonna be asexual" and came up with a better way to procreate through science.
 * The young Master at the age of 8? Sure it could be a Gallifreyan 8 but still.

The Time Lords gave everybody increased regenerations during the War
We know from the old series that they can give more regenerations than the usual 13; sometimes they need to take them from somebody else, but given the casualties, deserters, and psychological breakdowns associated with war, that isn't going to be much of a problem for people like the Time Lords. The Doctor was among those who got an increased regeneration count, which is why he now claims to have a total count of 507.

The Doctor aided in bringing down Osama bin Laden.
Proof? One of the Navy SEAL teams that raided Osama's compound captured a trove of computer drives and disks, yeilding a lot of important intelligence. They reported the capture with a pre-arranged signal: “Geronimo!”

The 12 regenerations thing is still canon and The Doctor used a regeneration up creating handy.
The Proof? In The Next Doctor, when 10 meets Jackson Lake, calling himself The Doctor, 10 exclaims that 'he must be the next one. Or the next but one.' This would be incarnation 11 or 12, because there can no longer be a 13th.

As a compromise in Amy and Rorys new bedroom
They have a king sized bunk bed. http://images.vrbo.com/vrbo/images/2f5bbb They exist

Tardises don't break down, they evolve.
Although we've always been under the impression that the Doctor's Tardis is an out of date reject, this has never seemed to be true, as his just gets more powerful and displays more and more unexpected abilities. We know Tardises are alive and can grow and repair, so how could the Doctor's ever be a broken reject? Tardises weren't taken in to be tuned up, they were taken in to be tuned down and keep their capabilities in check, and then scrapped when it looked they were getting a little bit too sentient. This would mean that the Doctor's Tardis isn't a flying screapheap, but, due to it's extended period of unchecked growth, more powerful than anything the Time Lords ever cranked out.

Tardises regenerate along with their Time Lord.
Besides the internal changes, which were somewhat explained in The Doctor's Wife, the Tardis' personality also changes in the same manner as a Time Lord, possibly even one intentionally compatable with their owner. It would explain the simularities between 11 and  and be a handy Hand Wave should someone write the Tardis differently at a later time. (As well as what's already happened in the Expanded Universe.)

Trakenites live approximately as long as a single Gallifreyan regeneration.
That is why the 14th Master had only aged as much as the 7th Doctor by the time the Fell Saltshakers blasted him in the TV Movie.
 * How long is a "single Gallifreyan regeneration"?

The Silence were in the Library.
Think about it.
 * No, the Silence was in the Library. In Day of the Moon, Amy was told she would "bring the Silence". As of A Good Man Goes to War, we know that.
 * Do Silents not count as "basic humanoid life"? According to "Silence in the Library" that was just the Doctor and Donna. Bringing the Silence seems to have more to do the the as-yet-revealed "fields of Trenzalore" deal.

Dorium's species is not naturally blue
Rather, its either a skin condition, the side-effect of a disease he has, or a natural consequence of unhealthy living. His saying that the doctor can't need him because he's blue isn't saying that the doctor only needs species that look exactly like Time Lords, but that the fact that he's been turned blue should indicate that he's less than useful.

Time Lords change sex during regeneration based on the sex of the people around them.
Certain fish change into the opposite sex of the fish around them. This keeps the male-female ratio balanced. Time Lords have a similar adaptation. The reason the Doctor keeps regenerating into a male is because most of his companions are females.

The Last Great Time War was the first event after the Big Bang
Two civilizations with time travel technology are at war. Civilization D launches an attack on Civilization G on Friday afternoon. The forces of G go back to Friday morning to pre-empt it. So D goes back to Wednesday, prompting G to launch a counterstrike the preceding Monday. As this goes on history is subtly rewritten, causing collateral damage to pan-dimensional beings and those that feed off temporal energy. Eventually every surviving fighter will arrive at the one moment in history which cannot be preempted; the first instant following the Big Bang in which the universe is big enough and cool enough to safely contain the combatants. In the post Time War continuity it is this epoch in which the final clash between the Time Lords and the Daleks took place, and which has been time-locked by the Doctor. Non-living remnants of these civilizations which survived down the ages informed advanced civilizations of these events, while beings that exist outside of normal time experienced it as another part of their "history."

The reason many Time Lords hid their names was to protect their childhood selves. How did they do it? By dying.
While most Time Lords are "dry, dusty intellectuals" as one villain put it, their wanderings and occasional interference could still gain them powerful enemies. And when is a time traveller most vulnerable? During their youth, before they became a time traveler.

So after looking into the Untempered Schism and spending a few years, decades or centuries at the Gallifreyan equivalent of Hogwart's, young candidates for the rank of Time Lord are taken in large batches somewhere outside of time and space to face an ultimate trial by fire. The only way to "survive" is to die and successfully regenerate for the first time. When the remaining students emerge they are literally unrecognizable, full-fledged Time Lords. All ties to their childhood are cut, their names are replaced with titles of their choosing, and they are assigned to a TARDIS crew and sent on research missions. The only place in the universe that contains a record of their childhood is inside their head. And they guard that final secret above all else, because to tell it to anyone who won't protect it as intensely as them is to risk being wiped from existence and rewriting the timeline.

The issue of powerful enemies is particularly relevant to three individuals: The Doctor, The Master, and one of the few Time Lords who's name is actually known; Rassilon, who by all accounts was just too scary to mess with. After all he was the "final boss" of the Tenth Doctor's tenure.


 * Wouldn't it mean that the 1st Doctor had already regenerated?
 * Yes, in this WMG Time Lords are granted 12 regenerations after the initial one which "graduates" them.
 * Correct me if I'm wrong, but doesn't a Time Lord gain their second heart after their first regeneration? I seem to remember that being an excuse for inconsistent biology between the 1st and the rest of the series, which would mean that The First Doctor is indeed his first body.
 * Hmm, combining this with an above guess, perhaps he did look into the Schism, but ran away immediately afterwards, for whatever reason?

The "drums" heard by the Master is a twisted version of the "Doctor Who" theme
On the last day of the Time War Rassilon broadcast the sound of a Time Lord's heart beats into the vortex so it would reach the Master no matter where he was in time and space, loud and insistent enough to drive him insane.

These four notes are also the bass line for the show's theme music, usually shown against a backdrop of the vortex.

doo doo doo doo, doo doo doo doo, doo doo doo doo, doo doo doo doo, doo doo doo doo...

The Sontaran clone race is a warrior caste Gone Horribly Wrong.
Okay, here's my theory. Millennia ago, the Sontarans and Rutans started their war. The Rutans were surpisingly overpowering, and the Sontarans needed to deal with them. So what did they do? Make their army proud warrior clones of their finest men with no fear of death. However they were too good at military strategies, and quickly overran Sontar. Over time, this has led them to lose sight of why their fighting, focusing on the glory. Why are there no women Sontarans? Sontar is sexist.

the Haitches were devoured by the crack in Aemilia's wall.

 * 'Whibbly, whobbly, timey-whimey ball' is NOW spelt 'wibbly wobbly timey wimey ball'. Where did all the haitches go? They were devoured by the crack in time, tlc.
 * When was it EVER given any spelling?

Timelord DNA is as adhesive as superglue
The Doctor kisses Martha so the Judoon's mouth-scan declares her in-human, and this is sufficient to fool the device. More notably, Lucy Saxon's lips apparently could provide enough of the Master's DNA to bring him back quite a while after she last kissed him. Maybe to do with the fact that Timelords are designed to live long lives?

Rory is part Time Lord
Why else would he be able to come back to life so many times?
 * Taking this theory and running with it: He's a future regeneration of Jenny. We've seen that she is at least capable of coming back to life without changing forms under some circumstances, but an even more lethal way of dying (Dalek lasers for example) might force her to. As to why Rory hasn't mentioned this he may be partially chameleon arched/had memories stolen, or, considering the emotional roller coaster The Doctor went through last time s/he showed up, might be doing so to spare his feelings.
 * Actually, he doesn't. Most of his deaths are visual trickery, faking the dead, dying in dreams. Stuff like that.

The Master's drums alter with enough time.
Self-explanatory, really. This is why the Master never showed signs of the drums back in the Classic series(out-universe, it's because Russel T Davies wants). Before becoming the villain we know and love, the drums would have been subtle. During the last of his original regenerations, they shifted into high gear. To the Master's mind, they sounded something like "You will rule all" or "Master of All." So the Master planned to do that. The first time he came back to life via Grand Theft Me, the drums became louder. This caused the Master to become more open about it. The sheer Large Ham and camp nature of the TV Movie Master is the result of yet another resurrection. When the Time Lords resurrected the Master, this caused the drums to become full-circle. Alternatively, the drums have been getting louder and more noticable as his personal timestream nears "The End of Time", where he finally snaps enough for it to be used by the Time Lords. or that they were always there but he never saw any need to mention it since The Doctor already knew. Admittedly the second one is a stretch...
 * I always assumed that either he would've turned out bad anyway and the drums simply didn't exist until post-time-war
 * Except they were sent back to him as a little boy before the Time War.

Faction Paradox is responsible for continuity errors.
Self-explanatory, really. Their devotion to create paradoxes has royally screwed up parts of the continuity. Examples include the "Looming" origin(despite the fact Eleven has a cot) and the Eight Doctor's timeline.

Time Lords were conscripted in the Time War.
Hence why none of them survived. All Time Lords not on Gallifrey or taking a vacation anywhere were summoned to the very beginning of the Time War. This was done by the Time Lords because a)they needed everyone they could get and b)it was the beginning If anyone refused, they were fed to House. Indeed, House may be one of the monsters created during the Time War-thrown back half a million years to avoid suspicion. This is the reason why the Master used a Chameleon Circuit: humans weren't part of the Time War, so his Yana personality could get out.

Time Lords change their name in the Academy.
Hence why the Doctor is referred to this, even by his fellow Time Lords. When a Time Lord passes the Academy, they change their name. This is a common practice, and fellow Time Lords hide their original names. Only those closet to them know. "Doctor" is his Academy name. The real mystery is his birth name.

Time Lords change their names to protect themselves from Carrionites
Before the Dybermen, the Daleks, and just about everybody else, before they even figured out Time Travel, there was an epic war between the Gallifreyan and the Carrionites. Gallifreyan warriors adopted new names to do battle, so they could not be magicked, and when the Carrionites lost, it brought on the dominance of science as we know it, instead of magic. After the war had passed into legend, the tradition of taking a new name was continued.

Mello is the child of the Doctor and River Song

 * This would explain the gun thing and why when a  shows up, everyone else tries to kill it, but Mello? He just calmly hands it a bar of chocolate. That is so Doctor.
 * This also explains why he - he knew the Death Note wouldn't work on him!
 * Plus, he physically looks like both River and the eleventh Doctor, as well as  and
 * Since he is the child of the Doctor and River,, that would mean...

Mello is a Time Lord. (It's already on the Time Lord WMG page, I am just posting a logical conclusion.)

 * He could have regenerated into Willy Wonka.

The Doctor's true age.
Given that the TARDIS said that they had been travelling for a good 700 years, we know he's older than that. To calculate his age, you'd need to add the amount of time a Time Lord can live naturally, before exhausting their first incarnation. We know that they can live centuries. During the Leisure Hive, being aged 500 years made the Doctor old. Thus, the current Doctor is at the very least in his 1300s. He has chosen to be 900-ish because of some Noodle Incident, the Time War ate centuries off his life, or just liked to feel younger.
 * It could be a bit like lying about not yet being forty. The Doctor having a minor mid-life crisis is a rather entertaining idea, particularly in light of the minor pissing contest he has with anyone else's (Jack's) methods of time travel.
 * I'm not following the figures here. Is it ever said that the Doctor recently stole the TARDIS in An Unearthly Child.

Gallifrey is locked in a linear time stream

 * When the Time Lords were first developing their ability to travel through time, they limited their travel to Gallifrey. This created a huge snarl of paradoxes, random bouts of overpopulation in certain time zones, future and past Lord Presidents arguing over who had more authority, etc. So to solve this, they locked Gallifrey into a single linear timeline to keep anyone from changing Gallifreyan history. Anytime you travel to Gallifrey, no matter what year it is in the outside universe, it is always the "current" year on Gallifrey. That's why the Doctor never has to ask WHEN he arrived on Gallifrey, or who's on the High Council, etc. The only time you can time-travel on Gallifrey is when the Time Lords themselves bring you forward, such as the Three Doctors and the Five Doctors serials.
 * So when Gallifrey was destroyed in the Time War, that's why it ceased to exist anywhere throughout time.

The Literary Agent Hypothesis is correct, and is in fact why The Doctor habitually picks up Companions from years in which the show is being broadcast
The Doctor sells his stories to the BBC, and, in exchange, the BBC makes sure ex-Companions get enough royalties to live comfortably on and are looked after if need be.

The Time War has fundamentally screwed up the Eighth Doctor's timeline.
While the Time War itself could not be altered, that doesn't mean everything before it wasn't. The radical alterations to history would've affected even the Time Lords' own histories. One of the most affected was the renegade Time Lord, the Doctor. Given his experience on other planets, it could amount to a lot. Since the Eighth Doctor was the one who entered the Time War, it altered his history the most.
 * Is this related to his timespan in comics, novels and audio?

Wilf really is the Doctor's father.
Some time during the Seventh Doctor's lifespan, the Doctor's father vanished. Everyone assumed he died, but in reality it was a Noodle Incident with a Chameleon Arch. Wilf was likely reverted to an child, and spent his time growing up on Earth. It would explain how the Mysterious Woman, who Russell confirmed as the Doctor's mother, could know Wilf so well. In order to find him, she may have used a Chameleon Arch as well. I add that only to finally explain the "half-human on my mother's side" thing.

The Master is in the closet.
It's clear as day.
 * The Master is in love with the Doctor, despite their opposing moralities. And the same for the Doctor. The moment the Doctor became a woman, they hooked up and lived happily ever after. If Its You Its Okay...
 * When he was Harold Saxon, he had to get the women on his side. He could not let his preferences damper his sexiness. And it worked.
 * His wife is The Beard. It's likely he never touched her, and was busy having delicious Foe Yay with the Doctor. Possibly even psychic sex, since the Doctor became really old. Lucy killed him because of this.
 * Almost canon; in Time Crash, Five asks Ten if the Master's still has that beard (referring to the literal beard both Delgado!Master and Ainley!Master have). Ten replies: "No, well, a wife."
 * Foe Yay. Foe Yay. Bountiful, delicious, slash-fic fuelling Foe Yay. The kind of Foe Yay that gives us plenty of Rule34 Master/Doctor.

All actors, who played the Doctor, are not actors
They really are the Doctor. The reason he can be seen in other shows is that he's trying to wave to us out of Television and Audio Books.
 * So...he married his own daughter, then?

The show Doctor Who is run by the Master
It's all a scheme to distract the brightest young minds of each generation from doing their homework, so they won't grow into potential members of the Resistance against his universe domination. We know it works because you're here, so desperate for more Who that you're reading this, and not doing whatever you should be doing. But why, you ask, would the Master make the Doctor the hero of the show? Because the Master is a Card Carrying Villain, aware that it's much easier to write what you know and recount actual happenings. BUT each actor who plays the Doctor has actually been a near twin of some regeneration of the Master, and vice versa for the actors of various villains looking like actual regenerations of the Doctor. Thus, if a fan were to meet the real Master, they would react as though he were the Doctor they knew and loved, and if they met the true Doctor, they would mistrust and fear him. Because the Master is Crazy Prepared!

The Eighth Doctor pulled the trigger on the Time Lords
Having to go from dashing adventurer to soldier was very likely an upsetting process. He went through as much if not more trauma than any other incarnation, and became even more disillusioned, if that were possible, with his fellow Gallifeyans. When "the Moment" came, the only thing that gave him pause was wondering if he could live with himself after killing his own people; he went through with it when he realized that, technically, he wouldn't HAVE to. The battle Nine was born in was the last of the Time War. This also explains why
 * The Ninth Doctor didn't know what he looked like.
 * He couldn't let the Delta Wave loose
 * He struggled with how much he wanted to be his old, human liking self and his protective, "stupid ape" persona.

The Companions don't care nearly as much about the Doctor as he cares about them.
I can't be the only one who's noticed that whenever one of the Doctor's friends gets the slightest bit hurt (like when Rory got knocked down in "The God Complex," the Doctor always comes running like a mother trying to protect her babies. But whenever the Doctor himself gets hurt (and he usually gets more seriously injured then his friends do), the companions are upset, but almost never to the point of running over and checking on him, unless they think he's about to die or something.

I admitedly haven't seen much of the classic series at all, so it may have been different then. I'm also a little hazy as to if they were protective of him during RTD's years (I remember in "Utopia" that Jack grabbed the Doctor to keep him from falling when they opened that door that lead to a dead drop, though). And yes, I know Rory died to save him from getting shot in "Cold Blood," but like I said, it's not that they want him to die- they very much don't. But they don't care about him getting injured much at all.
 * Rose and Martha seemed really protective towards Ten. Especially considering how long Martha looked after him in "Human Nature"/"The Family of Blood". Was that just me?

The Doctor is a Space Master...
...and the Police Box is his DARSIT.

Time Locks happen when time gets to wibbily
To many instances of crossing timelines, and the universe says F it

Inspector Spacetime was the show that was premiering during Remembrance of the Daleks.
Though it sounds like the announcer is about to say "Doctor Who", it's actually just the name of the first actor, whose name happens to start with sounds somewhat like "Doctor".

Doctor Who? will be asked right before Matt Smith's end as the Doctor.
It will be asked at the Fall of the Eleventh. Silence must/will fall, or The Doctor must/will die after it is asked. The question will be asked, the eleventh doctor will fall/die. None of these would be prophets mention regeneration, do they?
 * Could also explain why the attempt to kill the Doctor before this. The church seems to worship the Doctor. The Byzantine incident has him, indirectly, refereed to as a good man. If the Doctor-Donna/Handy incident theories of that being a used regeneration are true that means the Valeyard is coming. He is coming after the twelfth regeneration, not Doctor. The question being asked will herald the Valeyard's rise.
 * Not necessarily. The Valeyard, if I remember correctly, is prophesized to exist between The Doctor's Twelfth and FINAL regeneration, not his Thirteenth. Since nobody's going to limit The Doctor's regenerations anymore for fear of being personally declared an enemy of state by The Queen, all this means is that 12 is the first Doctor with the potential to become the Valeyard. And honestly, either The Valeyard will be used as a recurring villain/another reason for The Doctor to hate and fear himself, or The Doctor will briefly become The Valeyard, somehow temporarily lose his remaining regenerations, do everything that The Valeyard does canonically, get snapped back and regain his regenerations.

Susan Foreman is the daughter of the Doctor and River Song.
I'm frankly surprised at not seeing this theory earlier on the list here.
 * But she's the Doctor's granddaughter.
 * Maybe she only claimed to be his granddaughter because she came from the future of his personal timeline.

The show isn't fictional; it's a dramatization of events which occurred in another dimension.
Obviously our world is another alternate universe that is somehow sealed up and completely separated from the Whoniverse...well, almost completely. Some people from the Whoniverse came here through a rift and, knowing that people would never believe their crazy stories, created Doctor Who in order to subliminally warn people about what lay in the other universe. That way, if another rift ever opens and aliens start pouring in, the loyal and informed fans will know what to do.

Omega is the Could Have Been King.
Omega could have been the head honcho of the Time Lords, but ended up being thrown into an antimatter universe, supposedly by Rassilon himself. While in his realm of nothingness, he built his army of Meanwhiles and Neverwheres (their names being plays on the idea of nonexistence) out of antimatter and jumped into the Time War to get back at his enemies while they were busy fighting.
 * And because major villains never die in this show, he'll be back for a season finale... played by Benedict Cumberbatch.
 * And not just any season finale, but the season finale for the 50th anniversary. They've set up the pieces with the Church having an Omega as their symbol. Think about it;

The Cybermen from "Blood of the Cybermen", "The Pandorica Opens", "A Good Man Goes to War" and "Closing Time" are of Mondasian origin

 * Partially confirmed. While they look almost exactly the same as the Cybusmen, with minute differences, the Cybermen from "Closing Time" were painstakingly pointed out to be of the Mondasian variety.
 * Alternatively, the Cybermen from "The Pandorica Opens" are of dual origin. Whilst the Cyber-Leader was a Cybus Cyberman, it was a Mondas Cyberman ship used. Ergo, both Cybus and Mondasian Cybermen were part of the Alliance. We saw the Cybus Cybermen at Stonehenge and a Mondasian ship in the sky. The Cybus Cybermen escaped the Void due to the Time Cracks and the Mondasian Cybermen had probably already joined the Alliance.

Rassilon was possessed by Morgoth
When Morgoth was thought to have been cast through the Doors of Night, he actually went through The Time Lock and into the last days of the Time War. Because of his absurd power and Timey Wimey Ball he was also able to possess Rassilon before the time lock and attempt to initiate the final sanction, which he knew would end his enemies back on Arda. Dagor Dagorath will be the hell that inevitably breaks loose when The Lock is broken (As it must be since The Master has Joker Immunity), The Doctor manages to stop the Final Sanction but not the return of the Time Lords and the war's other atrocities, and "Rassilon" brings the full force of the Last Great Time War to Arda to the greatest extent that he can. Eventually, because of his Time War related mucking about in Ardan history, the Free Peoples will develop space travel, Turin will siege The Citadel on Gallifrey (Any time travel related issues with it having been defeated because of captured technology and everyone being distracted by the Daleks) and slay "Rassilon" thus fulfilling the prophecy. Alternatively...
 * The Doors of Night? The entrance to the antimatter universe. This, of course, means that Gallifrey is Arda. I'll let you think about that for a few minutes.
 * WIN. All of it.

Death Comes to Time is canonical.
The Doctor is clever; it's not outside the realm of possibility that he'd fake his own death to try and slip into obscurity. In fact, that's exactly what he did in

Ace is Rory's mother
We never see Rory's parents (at least not yet) and Ace has apparently started a charity, but we don't know why she left.
 * Pretty quick time frame to settle down in, and that's assuming she didn't land in the mid-to-late 90s.

Amy will die midway through Season 7.
This series just gets bleaker and bleaker as it goes on. Moffat has dedicated his reign to shaking up the established Doctor Who tropes, so killing off a well-loved companion without some timey-wimey plot twist to bring them back just seems like the next logical step for the series, and with all of Rory's deaths so far, killing him again would just seem cheap.
 * Doctor Who has always been big on tragic irony, but this would just be brutal. Rory would have to live forever without Amy. Imagine how he'd break down if she does go. Though it'd be sad and beautiful, it's way too dark for what is essentially a kid's show. They'll probably both survive their forthcoming Angel encounter, but be separated from the Doctor forever in some way. Remember, the overarching theme of Doctor Who is the triumph of optimism.

The Doctor just kinda sucks at regenerating.
So far, he's the only Time Lord we know who can't control his regenerations. We see that the Master, River, and Romana have all determined what they'll regenerate into beforehand. Romana goes as far as to regenerate multiple times without dying and the Master stopped his entirely one time, yet the Doctor always seems to get randomized results. Conclusion: he doesn't really have the whole process down.

The personality of each regeneration of the Doctor derives from how the First Doctor was at the time of his death.
Think about it, at the time of his death, One had pretty much established himself as someone who will always do the right thing and defend against evil. This carries over into ALL his future regenerations. Some of their traits are different, but their core personality, which was One at the time of his death remains the same.

The Doctor will meet Susan Foreman, his granddaughter, one more time.
He goes to visit her when he dies for real. His very first companion will also be his last.