Specific speculation on the Classic Series and/or the TV Movie goes into Doctor Who Classic Series. Specific speculation on the Eccleston era onward goes into Doctor Who New Series Specific speculation on the latest series goes into Doctor Who (with spoilers) (contains spoilers). Archived confirmed/Jossed speculation for the final Tennant years post-"Last of the Time Lords" is in Doctor Who Series 4 Specific speculation of Matt Smith's first series goes into Doctor Who Series 5 General speculation on Doctor Who goes into Doctor Who Whole Series
The cubes from "The Power of Three" imitate their surroundings.On their first activation, all the cubes did something different.
Miss Kizlet was taken over during the Web of Fear
The Ice Warriors will attempt to create a nuclear war in The Cold War.
Journey To the Centre of the TARDIS will involve something imprisoned in the TARDIS breaking out
The Whispermen are related to the Silents
In The Rings of Akhaten the Doctor will make a reference to Pyramids of MarsJossed.
Clara is impossible because:
The TARDIS knows who and what Clara is, and sees her as a threat to The Doctor
The Fall of the Eleventh and the Fields of Trenzalore will occupy the 7th season finale, but have little to nothing to do with the 50th Anniversary.Reading the summaries of upcoming episodes suggests that the big Question will be asked in the series 7 finale, but the 50th Anniversary is indicated as a separate televised event. The summaries may be misleading, however.
The Old God of Akhaten was one of the Great Old Ones
Each episode will have a Chekhov's Gun for the next episodeStarting with The Bells of Saint John each episode will set up Foreshadowing for the next episode.
The Doctor was lying when he said that the HADS was the reason the TARDIS disappeared at the beginning of "Cold War".
Songs will play a major role.So far there have been 2 stories that have mentioned songs, with the Rings of Akhaten and Cold War.
Clara is a clone and "Orphan Black" is a ripoff of her backstory.For some reason that we don't know yet, she was cloned, with her duplicates scattered throughout space and time. BBC America picked up "Orphan Black" to lead us astray!
Clara is Susan Foreman's descendant.In The Rings of Akahten, during one of the flashback scenes, Child!Clara can be seen wearing a shirt with two hearts on it. In that same episode, Susan is directly referenced for the first time since Five Doctors. The Doctor says himself in Curse of Fenric that he doesn't know if he has any family, meaning he doesn't know what happened to Susan. It's entirely possible that everything inexplicable about Clara can be explained by her being part Time Lord, and the Doctor just doesn't realize it yet.
There's a more personal reason why the TARDIS dislikes Clara.There's mention of an unusual/an averted love triangle in the future, between the Doctor, River and Clara (which makes me think River/Clara). Perhaps she's still prejudiced against "Impossibilities" (i.e. Jack)and wants to protect her daughter from falling in love with one (Clara)
The Doctor's Name will be The Unreveal.He'll end up telling River because that's a Foregone Conclusion, but the audience and possibly every other character won't actually hear it.
The Doctor's name is "Please"
The Special Weapons Dalek/Imperial Daleks in the Dalek Asylum turned Oswininto a Dalek. Being Daleks, one wonders why even the insane Daleks converted Oswin into one of them. However members of the Asylum included the Special Weapons Dalek and Imperial Daleks, who are people converted into Daleks, which along with their loyalty to Davros is why they caused a Dalek civil war. Since they started out as non-Daleks and didn't go crazy in their first appearance due to this, they'd see nothing wrong with converting Oswin. Of course this raises the question of why the Renegade Daleks didn't kill them, but that's either because they didn't know that they were impure or that they were put there by the Imperial Daleks.
Clara is RiverIn the Journey to the Centre of the TARDIS episode, the doctor is teaching Clara how to fly the TARDIS. Also, Clara finds a library in the TARDIS and apparantly finds out the doctor's real name. It's been mentioned that River knows the doctor's name and how to fly the TARDIS. So based on that, Clara could be River song (somehow, through some timey wimey thing...)
River is the author of the History of the Time WarIf it were a Galafreyan tome, it would be written in Galifreyan, which, as River pointed out in "A Good Man Goes to War", the TARDIS won't translate for others. If it were just written by any old historian, they wouldn't have known The Doctor's real name. And if it were written by The Doctor himself, he would have omitted that part, or at the very least written it in first-person format. It is likely a one of a kind volume, written by Dr. River Song, for The Doctor himself.
Strax will die in The Name of the Doctor
In Nightmare in Silver the Doctor will be partially Cyber-Converted and revive the Cybermen while like this
Jenny from Victorian London is the same Jenny that is the Doctor's daughter
The Claras from Asylum of the Daleks and The Snowmen are clones or split timeline versions of the Clara currently with the Doctor.
The Whispermen are the opposites of The Silence
An amusement park machine will create a duplicate Doctor in Nightmare in Silver
The Whispermen are working with the Great Intelligence
The man in the "Next Time" trailer for "The Name of the Doctor" is a young First Doctor.The preview has the Doctor saying he's crossing his own timeline in a way the TARDIS doesn't like. Going far enough back possibly to before the Doctor was stolen by the TARDIS (and thus risk altering that event) would definitely suffice.
The Whispermen have some connection to secrets
Clara is a physical manifestation of an ideal Companion.
The Name of the Doctor will lead into the 50th Anniversary
The Great Intelligence will still have a link to Clara or the Doctor
Trenzalore was effected by the Time War
The Whispermen are blank beings
The series finale confirms the "Morbius Doctors" as actual previous incarnations
The Gallifreyan Clara worked on the TARDIS.One of Clara's numerous "echoes" through the Doctor's timeline met his first incarnation as he was stealing the TARDIS on Gallifrey. This Clara must have been Gallifreyan, perhaps a Time Lady, and have a job related to faulty TARDIS-es. She did something the TARDIS is still angry about. Also, Fridge Horror, the Time War claimed Clara as one of its victims.
The Real Ninth Doctoris the one who actually ended the Time War. Since the current Doctor refuses to call the Doctor just revealed as having broken the implied promise in the name he chose, it seems likely that what he did in the name of peace and sanity is something the others could not: act without being hampered by the need to save everyone.
Alternately, John Hurt's "Doctor" is an older Eighth Doctor. One regeneration, he just cast aside his name at the start of the Time War and died of shame for what he did to end the war (involving killing the other Time Lords), consequently regenerating into the Ninth. Same result as the above, though it doubles as both a Take That to that specific incarnation and as a means to give that incarnation closure.
There is a version of Clara that helped the John Hurt Doctor. And she's still alive! Or it is his greatest failure.
The John Hurt Doctoris The Valeyard.
The Great Intelligence is Nyarlathotep.Granted, the EU claims he's Yog-Sothoth, but the Great Intelligence doesn't really share much in common with Yog-Sothoth. He does, however, share a lot with Nyarlathotep: both take many forms but seem to ultimately be pure consciousness, are defying physical laws while taking human form, highly manipulative and unlike fellow Outer Gods do not possess Blue and Orange Morality-they recognize humanity and love screwing around with them. Part of his beef with the Doctor is that he's a "mere" Time Lord who manages to, as he sees it, out-manipulate him and step in his territory. The fact that the Doctor(and the Master, for that matter) resembles Nyarlathotep makes him angrier still.
Matt Smith isn't going to leave the show.It's a work.
The John Hurt Doctor is the 13th and last incarnation.In his future, the Doctor fights in the war on Trenzalore, and dies in it. By this time, he no longer uses his alias of the Doctor, having turned to the dark side as foreshadowed by the Valeyard. Since we know that John Hurt won't end up as the 12th, and due to the (still not done with) 13 regenerations limit, it would seem that before (or while) regenerating into the 13th, he becomes a self-righteous, dark man, who no longer fights to make people better, but for his own sake.
The reason the Cybermen are like the Borg is due to Assimilation2
The John Hurt Doctor fought in the Time War and sacrificed an innocent race. He didn't end it, however.The Ninth, Tenth, and Eleventh Doctors have all copped to doing what they felt was necessary to end the Time War and save the rest of creation. They feel guilty about it, but none of them feel that it was something that would make in necessary to stop calling himself The Doctor. When the Eleventh thought the only option to save Spaceship UK and the space whale was to lobotomize the whale so it wouldn't feel pain, he said he'd have to find a new name. Knowingly sacrificing an innocent is where he draws the line. From a medical perspective he's doing harm and therefore can't be a doctor. The Hurt Doctor did something similar. It's probably the event that made him decide to regenerate into Eccleston and put an end to the Time War so that universe and The Doctor could go on.
Trenzalore is where The Valyard died.In his very last life The Doctor becomes The Valyard and goes on an truly epic plot to takeover the universe, cashing in all the good will of all his past lives and calling in favours from all his old allies. He is exposed and eventally taken down by an alliance of his former friends and companions and killed, for real, on Trenzalore.