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The televised series of Doctor Who and its spin-offs (Sarah Jane Adventures, The Class, etc) take precedence, and I don't think I have to explain why. Only some charity episodes are considered to be within continuity.
This will less be based off what contradicts which story, and more on author intent/connections to canon. It should be noted that everything is within continuity, but there are levels of canon.
Secondary Cano
To start off with, Big Finish is definitely canon, they've said this themselves and the BBC seems to agree with them. Their lisence only allows them to base their stories off the TV series or produce original works (see point 2), and they're considered to be "in the world of Doctor Who."
BBC/Virgin Novels
According to this, BBC and Virgin Novels originally were more self-contained to appease fans and direct connections to the TV show's continuity was discouraged, but eventually they evolved encompass a much wider scope after growing in prominence and shifting into canon. The creators also implied the Virgin New Adventures are canon: "Produced by arrangement with BBC television, this first-ever series of original Doctor Who novels will continue where the 1989 TV series left off."
Stories like Engines of War, Twelve Angels Weeping, Time Lord Fairy Tales and other BBC published New Who Novels are considered cano and are generally based off ideas from the TV show, plus they keep a much better sense of continuity than some of the older novels. It's also clear that stories like the Quantum Archangel are made to be form-fitting with canon (though it inevitably contains some contradictions), containing references from the most obscure to the most popular of Doctor Who media, while All-Consuming Fire is its own story.
The older BBC cares less about keeping continuity than the Virgin Novels, according to Love and Monsters: The Doctor Who Experience, 1979 to the Present, and even planned to produce blatantly contradictory novels before these were scrapped for various reasons. But Doctor Who Magazine calls these novels (likely including the Target ones below) a step down from the TV show's continuity, but still canonical.
The only real exception I could see to this is the film novelizatio, which was based off a previous version of the script and has some incredibly drastic differences and downright contradictory events.
It should be noted that Virgin Books is a successor of Target novels and under the same company.
IDW/Titan Comics (and some Big Finish)
IDW and Titan are lisenced publications that seemingly have a similar canon in some way, shape or form. According to Titan Comics, the Torchwood Comics are in continuity with the Torchwood Big Finish Audio Dramas.
Target Novelizations/The Scripts (Barely)
Despite not being produced by BBC itself, the Target Novelizations are officially licensed and considered to be "the only way most fans of the series could relive the television adventures", as well as reproductions of their television counterparts rather than recreations (albeit with many differences). Aditionally, most of these stories were written by the scrip writers of these original episodes.
In an interview with Tom Spilsbury, Steven Moffat has claimed that differences between the source material and the novelizations are a product of memory, which Russel T. Davies seems to imply. Changes from the television stories can also be the result of re-integrations that were planned but never made into the final product, this is likely the reason why the Myrka in Warriors of the Deep (a story heavily affected by budget constraints and writer strikes) is so different from its novel counterpart, an addition that was also applied to the comics.
Unlike Target Novels, the Scrips are based almost directly off the actual episode scripts from Doctor Who, but they do diverge a bit in dialogue and actions.
Faction Paradox
Faction Paradox takes many ideas from BBC and Virgin Novels, particularly the latter, but it's a standalone series that contains references to content in Doctor Who and changes names make it seem more mystical and set apart from sci-fi elements. For example, the Time Lords are referred to as the Great Houses, the Great Vampires are called the Yssgaroth, and TARDISes are almost always referred to as timeships.
The Faction Paradox audio series is produced by BBV (see this page) under an agreement with Lawrence Miles, who had resigned from writing Doctor Who to produce his novels. Much of the series also takes place in a timeline that The Doctor aborted by destroying Kasterborous and Gallifrey.
However, canonical stories contain many references to Faction Paradox stories, such as Ghost Clusters, which have only been mentioned in The Book of the War. There's also some other references, but they're very few and far between because of how obscure the whole Faction Paradox series is.
Comic Strips
A lot of these stories are self-contained and don't break continuity (a lot of them do as well), but some these reference nebulous bits of canon. The best example I can think of is the Second Doctor's Regenerationn; books, Audio Stories and Two Doctors (a canonical TV story) claim he didn't initially regenerate at the Time Lords' hand on Gallifrey, and worked for the Celestial Intervention Agency. One comic strip shows him regenerating into his Third Incarnatio after being attacked by Scarecrows from the Time Lords that were used to carry out his trial and punishment. However, this seems to have been largely dropped from existence.
Dalek Chronicles
The Dalek Chronicles in a time period before Davros' changes, hence they are non-canon, but the Daleks seemingly reached a technological state of advancement comparable to this at some point, so they'd still be usable for the Daleks themselves. It's also clear that stories like The Daleks and Dalek Invasion of Earth, which takes place a million years before the former, are still within Doctor Who continuity, events from these stories even mentioned in Remembrance of the Daleks where Davros is alive.
BBC Adventure Games are cano at least on the same level as the books, if not the TV series. They also appear to be self-contained and don't continuity too massively (there's arguments you could make, but they'd mostly be based on conjecture).
According to the wiki, these games are non-canon.
Unofficial Releases
Time's Champion was pitched, but rejected by the BBC. It's therefore considered fan fictio. However, there's many references to canonical elements from The Quantum Archangel and Millennial Rites because it was written by Craig Hinton and Chris McKeon, the latter of whom did most of the work according to Who Cast #84. It also marks the first appearance of the Menti-Celesti known as Death, Life, Time and Fate, and continues the champion idea (with Kronos being a champion of life) from The Quantum Archangel.
Here's a list of unproduced novels.
Notes
Despite author intention and canon, Doctor Who is an extremely long-running series with multiple contradictions. The 12th Doctor himself canonically explains in the TV series that time is in a constant state of flux even without the existence time travelers, giving a reason for this. The Thirteenth Doctor also explains in Orphan 55 that the future is ever-changing and even the ones they travel to can potentially be alternate timelines, and time is stated to be extremely malleable in The Unquiet Dead and Blink. Often, stories are chosen for their prominence, so something like the qualitively superior Genesis of the Daleks would most certainly be more prominent and go-to than Twelve Angels Weeping.
It should be noted that a lot of what characters say are either off-hand or anachronisms. For example, if someone called Fenric 5,000 years old in his first appearance, then that's clearly retconned by both the TV series and Extended Universe. The Doctor himself has also admitted to exaggerating in the Crystal Bucephalus and once claimed, off-hand, that he has 507 regenerations. Recently, The Timeless Childre has retconned the entirety of Doctor Who history.
Result
The profiles contain a couple mentions from Time's Champio, such as the Eternals and Chronvores being equal, but that's not exactly contradicted by canon and supported by The Quantum Archangel.
The only specific change I could see is removing Type 9 Immortality from the Elder Gods. This concept comes from White Darkness, where it states they originate and left their essence in their alternate home-universe known as the outer planes, which is highly contradictory.
This will less be based off what contradicts which story, and more on author intent/connections to canon. It should be noted that everything is within continuity, but there are levels of canon.
Secondary Cano
To start off with, Big Finish is definitely canon, they've said this themselves and the BBC seems to agree with them. Their lisence only allows them to base their stories off the TV series or produce original works (see point 2), and they're considered to be "in the world of Doctor Who."
BBC/Virgin Novels
According to this, BBC and Virgin Novels originally were more self-contained to appease fans and direct connections to the TV show's continuity was discouraged, but eventually they evolved encompass a much wider scope after growing in prominence and shifting into canon. The creators also implied the Virgin New Adventures are canon: "Produced by arrangement with BBC television, this first-ever series of original Doctor Who novels will continue where the 1989 TV series left off."
Stories like Engines of War, Twelve Angels Weeping, Time Lord Fairy Tales and other BBC published New Who Novels are considered cano and are generally based off ideas from the TV show, plus they keep a much better sense of continuity than some of the older novels. It's also clear that stories like the Quantum Archangel are made to be form-fitting with canon (though it inevitably contains some contradictions), containing references from the most obscure to the most popular of Doctor Who media, while All-Consuming Fire is its own story.
The older BBC cares less about keeping continuity than the Virgin Novels, according to Love and Monsters: The Doctor Who Experience, 1979 to the Present, and even planned to produce blatantly contradictory novels before these were scrapped for various reasons. But Doctor Who Magazine calls these novels (likely including the Target ones below) a step down from the TV show's continuity, but still canonical.
The only real exception I could see to this is the film novelizatio, which was based off a previous version of the script and has some incredibly drastic differences and downright contradictory events.
It should be noted that Virgin Books is a successor of Target novels and under the same company.
IDW/Titan Comics (and some Big Finish)
IDW and Titan are lisenced publications that seemingly have a similar canon in some way, shape or form. According to Titan Comics, the Torchwood Comics are in continuity with the Torchwood Big Finish Audio Dramas.
- Torchwood is Back, in an all-new ongoing comics series written by Captain Jack himself, John Barrowman! Captain Jack Harkness is back in Cardiff, and there's only one person he can turn to, the last person who expected to see him, Gwen Cooper! On the road, on the run, and under fire, can the pair put aside their differences and rebuild the heart of Torchwood, before its flame is stamped out forever? Even better, the new comics series is in continuity with the amazing new Torchwood audio dramas from Big Finish; join us both for the official continuation of the Torchwood saga!
Target Novelizations/The Scripts (Barely)
Despite not being produced by BBC itself, the Target Novelizations are officially licensed and considered to be "the only way most fans of the series could relive the television adventures", as well as reproductions of their television counterparts rather than recreations (albeit with many differences). Aditionally, most of these stories were written by the scrip writers of these original episodes.
In an interview with Tom Spilsbury, Steven Moffat has claimed that differences between the source material and the novelizations are a product of memory, which Russel T. Davies seems to imply. Changes from the television stories can also be the result of re-integrations that were planned but never made into the final product, this is likely the reason why the Myrka in Warriors of the Deep (a story heavily affected by budget constraints and writer strikes) is so different from its novel counterpart, an addition that was also applied to the comics.
Unlike Target Novels, the Scrips are based almost directly off the actual episode scripts from Doctor Who, but they do diverge a bit in dialogue and actions.
Faction Paradox
Faction Paradox takes many ideas from BBC and Virgin Novels, particularly the latter, but it's a standalone series that contains references to content in Doctor Who and changes names make it seem more mystical and set apart from sci-fi elements. For example, the Time Lords are referred to as the Great Houses, the Great Vampires are called the Yssgaroth, and TARDISes are almost always referred to as timeships.
The Faction Paradox audio series is produced by BBV (see this page) under an agreement with Lawrence Miles, who had resigned from writing Doctor Who to produce his novels. Much of the series also takes place in a timeline that The Doctor aborted by destroying Kasterborous and Gallifrey.
However, canonical stories contain many references to Faction Paradox stories, such as Ghost Clusters, which have only been mentioned in The Book of the War. There's also some other references, but they're very few and far between because of how obscure the whole Faction Paradox series is.
- Weapons were readied: chronal torpedoes, chronic tripwires, ghost clusters and parallel beams and living weapons that thought form themselves, and it was almost enough to make you believe in the Time Lord superiority again. - Twelve Angels Weeping.
Comic Strips
A lot of these stories are self-contained and don't break continuity (a lot of them do as well), but some these reference nebulous bits of canon. The best example I can think of is the Second Doctor's Regenerationn; books, Audio Stories and Two Doctors (a canonical TV story) claim he didn't initially regenerate at the Time Lords' hand on Gallifrey, and worked for the Celestial Intervention Agency. One comic strip shows him regenerating into his Third Incarnatio after being attacked by Scarecrows from the Time Lords that were used to carry out his trial and punishment. However, this seems to have been largely dropped from existence.
Dalek Chronicles
The Dalek Chronicles in a time period before Davros' changes, hence they are non-canon, but the Daleks seemingly reached a technological state of advancement comparable to this at some point, so they'd still be usable for the Daleks themselves. It's also clear that stories like The Daleks and Dalek Invasion of Earth, which takes place a million years before the former, are still within Doctor Who continuity, events from these stories even mentioned in Remembrance of the Daleks where Davros is alive.
- DOCTOR: Exactly. And ever since the Daleks were created, they've tried to conquer and enslave as much as the universe as they can get their grubby protuberances on.
- ACE: And now they want to conquer the Earth.
- DOCTOR: Nothing so mundane. They conquer the Earth in the twenty second century. No. They want the Hand of Omega.
- DOCTOR: So? Ace, the Daleks have a mothership up there capable of eradicating this planet from space, but even they, ruthless though they are, would think twice before making such a radical alteration to the time line.
BBC Adventure Games are cano at least on the same level as the books, if not the TV series. They also appear to be self-contained and don't continuity too massively (there's arguments you could make, but they'd mostly be based on conjecture).
According to the wiki, these games are non-canon.
Unofficial Releases
Time's Champion was pitched, but rejected by the BBC. It's therefore considered fan fictio. However, there's many references to canonical elements from The Quantum Archangel and Millennial Rites because it was written by Craig Hinton and Chris McKeon, the latter of whom did most of the work according to Who Cast #84. It also marks the first appearance of the Menti-Celesti known as Death, Life, Time and Fate, and continues the champion idea (with Kronos being a champion of life) from The Quantum Archangel.
Here's a list of unproduced novels.
Notes
Despite author intention and canon, Doctor Who is an extremely long-running series with multiple contradictions. The 12th Doctor himself canonically explains in the TV series that time is in a constant state of flux even without the existence time travelers, giving a reason for this. The Thirteenth Doctor also explains in Orphan 55 that the future is ever-changing and even the ones they travel to can potentially be alternate timelines, and time is stated to be extremely malleable in The Unquiet Dead and Blink. Often, stories are chosen for their prominence, so something like the qualitively superior Genesis of the Daleks would most certainly be more prominent and go-to than Twelve Angels Weeping.
It should be noted that a lot of what characters say are either off-hand or anachronisms. For example, if someone called Fenric 5,000 years old in his first appearance, then that's clearly retconned by both the TV series and Extended Universe. The Doctor himself has also admitted to exaggerating in the Crystal Bucephalus and once claimed, off-hand, that he has 507 regenerations. Recently, The Timeless Childre has retconned the entirety of Doctor Who history.
Result
- 1. Avoid the older novels if you can, preferably stick with the Television series, newer BBC novels, Big Finish audio dramas, comics, and canon games. However, the latter 4 are still canon until they're not.
- 2. Ignore unlicensed and unofficially produced novels, though Time's Champio appears to keep with continuity. Maybe references to it can be used, such as <insert character> being far more powerful than <insert character>.
- 3. Faction Paradox novels are self-contained and potentially aborted, so they probably shouldn't scale to the outer Doctor Who Universe. An exception is Compassion, who extends to the Eighth Doctor line of BBC novels.
- 4. Canon is partially based on prominence, which can be decided by different authors.
- 5. Take everything with a grain of salt, and look especially at portrayal. For example, The Doctor may have the power of affecting higher-dimensions without technology in one story, but the Time Lords are also omnipotent, born in the Six-Fold Realm and far superior to each and every Transcendental Species in the Doctor Who universe during this same story, meaning his power is likely exaggerated above what most media portrays it as.
The profiles contain a couple mentions from Time's Champio, such as the Eternals and Chronvores being equal, but that's not exactly contradicted by canon and supported by The Quantum Archangel.
The only specific change I could see is removing Type 9 Immortality from the Elder Gods. This concept comes from White Darkness, where it states they originate and left their essence in their alternate home-universe known as the outer planes, which is highly contradictory.
- 'No no no.' The Doctor shook his head, and pulled a bunch of grapes from his upturned hat, depositing them at Petion's bedside. 'As I told Ace, they can't be killed in this universe. They originally came from some other universe, other dimension ― one of the outer planes, most likely ― and part of their being still resides there. Another part exists in their physical form, but that can't do anything without the third ingredient.'
