Doctor Who/Fanfic Recs

Proof that the remaining 10% is worth regenerating for here.

These are recommendations made by Tropers for Doctor Who, all of which have to be signed to stay on the page. Feel free to add a fanfic of your own to the list, but remember to use the template found here.

You can also add to the current recommendations if you want. Refrain from posting Conversation in the Main Page though; that goes in the discussion page.

Doctor Who has a long history of fan-fiction in non-text formats; fan audios were being made in the early 1980s by some people who would later work on the show post-2005, including Nicholas Briggs.

Authors and Websites
The "This Time Round" Archive by various.
 * Recommended by Daibhid C
 * Now has its own Trope Page
 * Synopsis: A Meta Fic series set in a pub outside Doctor Who continuity, where the characters go between stories. And the surrounding town. And the creche, where the Spinoff Babies stay and have a storybook that forces their adult counterparts to act out fairy tales. And the High School AU, Primary/Elementary School AU, and Retirement Home AU.
 * Comments: Particularly recommended is B.K. Willis's To Die For series in which, free from the burden of her canonical personality, Nyssa is reimagined as an inventive psychopath with a grudge on Adric (who keeps coming Back From the Dead). It's much better than that makes it sound.

The Ten Doctors by Rich Morris
 * Has its own Trope Page.
 * Alternate Link to download the comics.
 * Recommended by cg12345
 * Synopsis'': A webcomic that is Exactly What It Says on the Tin. Ten Doctors, many companions, and just about every enemy from the TV series that wasn't dead at the end of their arc.
 * Comments: A fun read, although a little slow at times.

The Crossover Adventures by Aron Toman
 * Recommended by Silent Hunter
 * Synposis: Basically a bunch of audio plays where the Doctor (played by Toman) and some original companions, plus Frobisher, as well as characters from Buffy the Vampire Slayer, Scream and The Muppets.

The Way of Things by jlrpuck
 * Recommended by Kathryn Shadow
 * Synopsis: Crossover with Blackpool. Boiled down to its most basic form, The Way of Things is an extremely extensive series centering around the relationship between DI Carlisle and Rose Tyler.

Talk To The Hand Series by Wynter Eyez
 * Recommended by Fiasco
 * Synopsis: A hilarious series that details the adventures of 10.5 (aka Handy, 10th Doctor Duplicate) living in Pete's world and coming to terms with his strange genetic quirks while having fantastic and hilarious adventures. It starts with
 * 1) Crossed Wires, which is followed by
 * a Christmas special: A Glorious Mess
 * 2) Straight Up With a Twist
 * 3) This Immortal Coil
 * 4) Romantic Entanglements
 * 5) Coming Undone
 * 6) Why Torchwood Banned Recreational BodySwapping
 * Comments: Some fantastic humour is in here - also the author brings in well known and loved characters in a creative way and likes to turn some old cliches on their head. Really worth a read.

General Fics
''Stories focused on the family and the friendly relationships of the cast. Plot-focused stories or light day-in-the-life stories. Pretty much anything that isn't focused on romance.''

Peripheral Vision by LadyEliseB (crossover)
 * Recommended by LadyElise
 * Synopsis: Torchwood/Doctor Who Crossover - Imagines that Donna isn't the only companion to have had her memory wiped.
 * Comments:

Huntsman by Lizbee.
 * Recommended by Namta
 * Synopsis: The Tardis communicates with Martha in her dreams, sending her a warning.
 * Comments: Utterly, utterly beautiful and haunting. The Harry Potter references work really, really well..

The Slow Path, or Two and a Half Centuries in Two and a Half Days by Amy Wolf (AU)
 * Recommended by Ms Shaw
 * Synopsis: An AU on the ending of "The Girl in the Fireplace," where the Doctor takes The Slow Path back.

People Used to Dream about the Future by calapine
 * Recommended by theorc
 * Synopsis: The world has ended. This is a lie. Too bad no one told Rose, Jack, and the Doctor.

The Moment Has Been Prepared For by Lurky McLurklurk (character death)
 * Recommended by alliterator
 * Synopsis: Donna's granddaughter watches as she dies.
 * Comments: A brilliant piece of Fix Fic that's great for those suffering after the ending of "Journey's End" (major spoilers for JE, however).

The Care and Feeding of Tiny Humans (and slightly larger Time Lords) by Netgirl_y2k
 * Recommended by Cinna the Poet
 * Synopsis: The Doctor returns for little Amelia Pond.

Season Four by ARIA (AU)
 * Recommended by JadedLady
 * Synopsis: What could have happened had at the end of season three and the Doctor actually made good on his plan to imprison the Master on the Tardis and drag him around the universe.
 * Comments: As expected, there's oodles of slashy Foe Yay, especially towards the end (so be warned), but it's so well done that you'll honestly not mind. A rather fascinating Alternate Universe version of Nu-Who

The Doctors' Mission Statement by nichelle.hp
 * Recommended by Silent Hunter
 * Synopsis: Exactly What It Says on the Tin.
 * Comments: Very short, but very, very true.

Psycho Savior, qu'est-ce que c'est? by kalima
 * Recommended by cg12345
 * Synopsis: The Ninth Doctor rescues a screwed-up suicidal girl, and rescues a living piece of architecture.
 * Comments: This story features a pretty dark take on the Ninth Doctor, who was never exactly a sunshiney kind of guy to begin with. Fortunately the writer never forgets that the Doctor is, in fact, a Big Damn Hero which keeps the story firmly on the side of pretty damn good. Great acidic dialogue between nine and the girl (Emily), as well.

Flowers on Fire by etherati
 * Recommended by Loki
 * Synopsis: Author's summary: They burn, in the darkness and the light, circling round each other like binary stars just on the edge of nova. They both burn, but they do not burn the same. Theta, Koschei, and their successors.
 * Comments: Long one-shot, spanning from academy era to new Who series three finale. All I can say is really really good. Really.

The Women by Nostalgia (Mentions of femslash, potentially upsetting, abortion)
 * Recommended by Molly
 * Pairing(s): Martha/Lucy (but not the focus)
 * Synopsis: It is so sort that I can't really give any explanation without spoiling it.
 * Comments: It is a complete tearjerker and is so well written.

After Life by Amy Wolf
 * Recommended by D Mint
 * Synopsis: Rationally speaking, you know you’re not dead. Also, there aren’t eight other people in here, and you aren’t trapped in Jean-Paul Sartre’s vision of Hell. A Journey to the Center of the Mind during the early hours of his regeneration into the 10th Doctor, After Life is told from the perspective of the 9th Doctor. that looks into how the 9th Doctor blames himself and the 8th Doctor for the Time War, his previous eight selves' light treatment of the Daleks, and how the 9th Doctor tries to learn to forgive himself and the Eighth Doctor for destroying Gallifrey.
 * Comments: An awesome read. Written in Second Person POV... and it works.

A Different World by Lady Clark-Weasley of Books (AU)
 * Recommended by Ryan Lohner
 * Synopsis: In "Doomsday", it's the Doctor who gets trapped in the parallel world, leaving Rose alone. The TARDIS makes her into a Time Lord and she picks up the show's canon from there.
 * Comments: For most of season three this is a pretty rudimentary AU fic with Rose largely just cut-and-pasted into the Doctor's place. However, when the Master shows up the story suddenly clicks into high gear as we get a great and truly different take on the events of those episodes. It largely stays that way from then on.

From This Day To The Ending Of The World, by Ice Blue Nothing
 * Recommended by Nightsky
 * Synopsis: The TARDIS, with the freshly regenerated Ninth Doctor inside, crashes onto a planet at the end of the war. Nine tries to put his life back together.
 * Comments: What's that, you say? You want an Eight -> Nine regeneration story? That is completely awesome? Here you go, then.

Earthbound by StormWolf (AU)
 * Recommended by Sadistic Apathy
 * Synopsis: Set post Journey's End in the parallel world. Shows how Human Ten adjusts to living a "normal" life with Rose.
 * Comments: While the adventure part of the story isn't bad, the real brilliance is in the scenes showing the domestic side of life. It gets quite sappy at times, but manages to retain the Doctor's obliviousness and awkwardness in family matters.

Remodelling by earthdrago
 * Recommended by Newtype S 3
 * Synopsis: Captain Jack Harkness' chunk of TARDIS coral finally is large enough to turn into a real TARDIS. This attracts the attention of someone else...
 * Comments: A touch of Ho Yay can be found in here between Ten and Jack. Whether or not that's your thing, the fanfic overall is excellently written. There's also a little hand-waving in, but the whole thing is probably the best fanfic This Troper has read.

Ten Times The Doctor Met Sailor Pluto
 * Recommended by SAMAS
 * Pairing: None, unless you count friendship
 * Synopsis: Exactly What It Says on the Tin. The Doctor crosses paths with Sailor Pluto ten times in their lives. Understandably, it's a little out of order.
 * Comments: The order given is from Pluto's POV. The order named is from The Doctor's. Try reading it both ways.

Frozen Hearts by bibliophile1887
 * Recommended by Nightsky
 * Synopsis: Peri comes to terms with the Doctor's new incarnation while the Doctor tries to keep her from freezing to death.
 * Comments: It's quite lovely, a bit angsty, but very good; it really shows how much the Doctor cares about his companions, even after regenerating. I'm not sure if it is friendship or shipping, could be either.

Doctor Who and the Silver Spiral by Dr. Megan Argo
 * Recommended by cg12345
 * Synopsis: The Doctor and Martha observe a supernova.
 * Comments: Ok, here's where it gets interesting. The supernova in question is a real event, and Dr. Argo was on the team that detected its energy emissions. She wanted to do something that conveyed the excitement of the discovery in Layman's Terms, so she wrote this. And yea verily, it is made of win. Martha asks a few too many elementary questions, but Ten's voice is spot-on, and Dr. Argo's sheer love for the subject matter carries the story.
 * Also available in an audiobook format.

The Doctor And The King of Pop
 * Recommended by Love Is Weird
 * Synopsis: The Doctor has a poignant encounter with Michael Jackson, the legendary King of Pop.
 * Comments: This is a must-read for every fan of Michael Jackson. It pays tribute to him in a way you could never imagine. I chuckled a bit at some lines, but the ending had me in tears. Note: Never read this while listening to Heaven Can Wait. The floor will look like a river when you're done crying.

Stardust Girl by riversrunthroughme
 * Recommended by Suspicious Cookie
 * Synopsis: She's doing this to him because she loves him - well, some other version of him. The one in the real world - but she's doing this because she loves him. Really. Really, really. He'll understand soon. Just not right now. But he'll understand. Eventually, Rose Tyler will make him understand everything, even this.
 * Comments: Warning - this is a dark fic. A chilling take on what Rose and 10.5's relationship could turn into. Alternate Universe!Jack is positively terrifying. Definitely worth your time, though you may never look at Rose the same way again.

If I could turn back the hands of time by SillBrainFried
 * Recommended by inklesspen
 * Synopsis: Rose Tyler, 10.5, and Romana II team up to save the alternate Earth from aliens. There is a lot of bluffing involved.
 * Comments:

The Game by Vic Taylor
 * Recommended by: Purple Bouncy Ball
 * Synopsis: The Doctor and the Master play the Game, because by now, it is all they have left.
 * Comments: This is a short oneshot detailing the dynamic between the Doctor and the Master, narrated as if by someone telling a story. It is well worth the five minutes it will take you to read, and it is so far one of the only fics I've seen that can say so much in so few words. It is poetic, painful, saddening, pity-inspiring, and most of all, accurate.

And I Must Scream by Starling-Night
 * Recommended by Shupapa
 * Synopsis: Silence has fallen, but the Doctor is screaming in the dark, immobile and imprisoned. AU from The Pandorica Opens.
 * Comments: This fic answers the question - what if it isn't so easy for the Doctor to escape the Pandorica? Dark and chilling.

Children of Galifrey by Hand of Omega
 * Recommended by A Random Whovian
 * Synopsis: A series of drabbles featuring the Master and the Doctor as children. Can be considered slashy, but it's mostly friendship. Filled with Classic Who references and a lot of different genres.
 * Comments: An amazing piece of work, honestly. Great for fans of New Who and Classic Who alike.

Five Times Lord Braxiatel Had Occasion to Regret The Doctor’s Exile Very Deeply Indeed by x_los
 * Recommended by CookiesAreNice
 * Synopsis: Humour - follows an Expanded Universe character's increasingly irritating encounters with the Doctor
 * Comments: You don't need to follow the EU to find this absolutely hilarious - the lovesick Master, the Doctor completely blind to the chaos he causes, the one scene only visits by companions, and possibly the best humorous characterization. Just read the thing.

Alone by Melora maxwell
 * Recomended by dalekandrew
 * Synopsis: Enter the mind of the last Dalek.
 * Comments: An excellent novelization of the episode Dalek, as seen through the eyes of the titular Omnicidal Maniac Woobie, Destroyer of Worlds. It will pull your heartstrings.

Ordinary Hero by eriphi
 * Recommended by patrckred
 * Synopsis: The Rixxi's planet is quite nice. If you don't count the poison, the cannibals and the rain. Rory loves travelling with the Doctor. Sometimes. Occasionally. Maybe once or twice. Today just isn't one of those days.
 * Comments: Rory gets to rescue the Doctor for a change.

Painting Over Cracks by be-nice-to-nerds
 * Recommended by Analiza
 * Synopsis: When the cracks in the universe close, what happened to the Weeping Angels?
 * Comments: This fic makes heavy use of timey-wiminess, but the writing is good enough to keep it a readable and fascinating oneshot.

The Stalker Of Norfolk by Rich Morris and Hilary Doda
 * Recommended by Mugen Kagemaru
 * Synopsis: Corporal Beverly Powell, a known historian, has just joined UNIT, and is joined for lunch by the Third Doctor, who is rumored to have shut himself in his laboratory after Jo Grant left him. They get into a disagreement over Lord Robert Dudley, and decide to revisit the period to prove which one is right. As Beverly attempts to prove Dudley's innocence, a sinister shadow seeks the life of Dudley's ailing wife, Lady Amye Rosbart-Dudley.
 * Comments: All I can say is that it's definitely worth a read. Also, if you squint, you can spot the First Doctor at some point in the story! Good show again, Rich!

Turn Your Back by Singe
 * Recommended by:psyzygy51
 * Synopsis: Ten short stories showing the different Doctors' reactions to nudity. MUCH better than it sounds.
 * Comments: Gen with hinted Ian/Barbara, Liz/Brigadier, Sarah Jane/Four, Ace/Seven, Martha/Ten. Maybe. if you squint. Humor/fluff. You'll probably find at least one CMOF or CMOH.

Loving the Impossible by Dr. Christie
 * Recommended by: Blue Hospitality
 * Synopsis: The Meta-Crisis Doctor and Rose have been traveling for three years now in the parallel universe. What will happen when an old acquaintance, with a new face, appears on their TARDIS?
 * Comments: Eleven meets Handy, Amy and Rory meet Rose, and a mystery unfolds in the TARDIS. Low on shipping.

Demon's Run by x_Avarice_x
 * Recommended by: Enhas
 * Synopsis: An Alternate Universe Fic set immediately following the events of "A Good Man Goes To War", in which there is much more about River Song's identity that the Doctor will soon finally know. As River herself says, Demon's Run is not a prophecy... it's a legend.
 * Comments: Featuring cameos and tie-ins to past (pre-Moffat) episodes and companions, a very different take on River Song's early life that involves a Stable Time Loop, and a final and tragic showdown in which the prophecy is fulfilled. Everything changes from the moment that gives the Wham! Line of  name to the Doctor, and rapidly continues doing so from there. I don't tend to read very many River-reveal stories, but this one was well worth the time invested.

Night Terrors by Lyricwritesprose
 * Recommended by Completely Different
 * Synopsis: "People have called Rory Williams brave. He doesn't feel that way." A character study of both the Doctor and Rory, involving Household gods, psychic communications and a sweet little transdimensional tentacled Lovecraftian horror.
 * Warning: The author warns that although there's no violence, it does deal with pyschological horror, and could possibly deserve a 'mature' warning for it.

They Say by Lyricwritesprose
 * Recommended by cg12345
 * Synopsis: The oppressed rely on whispers. An outsider's POV on why this Insignificant Little Blue Planet just cannot be invaded.
 * Comments: "The planet isn't some sort of trap, or hellworld, or property of something unimaginable. It's just -- protected." Short and brilliant. I love how the Doctor's influence has turned Earth into both Nightmare Fuel for invaders, and a beacon of hope for those in need.

Sexy Dresses by Lyricwritesprose
 * Recommended by: cg12345
 * Synopsis: There is a reason why the Doctor has never had all that much luck repairing the chameleon circuit. TARDIS POV on why she sticks with the police box shape.
 * Comments: Perhaps she needs words. Reassuring words. Something to mark her as a friend, something that tells the primitives that she's useful and helpful and not going to hurt them. A sign, a marking-- She brushes by a booth on the corner of a street, and the possibilities explode. If you liked "The Doctor's Wife" even slightly, you will fall in love.

ROPE by kalima
 * Recommended by: cg12345
 * Synopsis: Tegan misplaces her key. She did not have a good time losing it. The Doctor sets out to retrieve it, and, in the process, changes a young man's perception of himself, and his place in the world.
 * Comments: Wow. Kudos to the author for making FIVE freaking terrifying without him seeming out of character. Seriously. He never raises his voice, he's never anything less than exquisitely polite, but the whole time there's just pure, Papa Wolf, Oncoming Storm fury lurking underneath. Beware the Nice Ones, indeed.

Doctor Who: Plastic Murder (prologue here and epilogue hereby Duke Nukem 2417
 * Recommended by: mortimermcmire
 * Synopsis: In this sequel to "Doctor Who: Plastic Nightmare", the Autons invade the city of Birmingham again, and it's up to the Third, Fifth and Eleventh Doctors---along with some old friends and a few new allies---to stop them. Brings back most of the original characters from "Plastic Nightmare", and introduces some new ones---as well as several Auton variants that have to be seen (or read about) to be believed. A third story---Plastic Legacy---is in the works.
 * Pairing(s): Mainly between original characters; the obvious Rory/Amy romance is also mentioned occasionally.
 * Comments:

Doctor Who: Plastic Nightmare by Duke Nukem 2417
 * Recommended by: mortimermcmire
 * Synopsis: The prequel to Plastic Murder, Plastic Nightmare centers around the Fifth Doctor racing against the clock to stop the Autons from taking over Birmingham. Features well-written original characters, a pretty cool battle sequence at Swannies (an actual British shopping center) and is generally one of the better Auton-based fanfics around.
 * Pairing(s): Mainly between original characters, namely James/Alex and James/Keeley.
 * Comments:

The Forgotten by A Ks-on-show
 * Recommended by praguespring
 * Synopsis: A young Australian woman named Sophie is forced to rely on someone for the first time in her life when the people around her start vanishing, and her universe literally begins to collapse. Her only hope is a man that calls himself the Doctor.
 * Comments: The first in what looks like it'll be a rather long series. Featuring a new Doctor and a new companion, this story spends a lot of time introducing them. Interesting characters, even if the prose is a little boring. Give it a look! You might even enjoy it.

Boxing Day by Lyricwritesprose
 * Recommended by Joysweeper
 * Synopsis: While trying to cope with grief and survivor guilt, Wilf meets the one person he never wanted to see. (Characters are Wilfred Mott and the Eleventh Doctor.)
 * Comments: Marks itself as Fix Fic looking at Ten's fear of upcoming regeneration and what happened with the Family of Blood, but it doesn't feel anything like shoehorned and obvious like a lot of those I've seen. There's also the line "I may be a story, but that never means I'm not real," which I just adore, and the mood changes which all seem so fitting.

Invisible Road by Lyricwritesprose
 * Recommended by Joysweeper
 * Synopsis: It. Is. Defended. Companion piece to "They Say", but it can stand alone.
 * Comments: It's not who you'd think it is  and it's awesome.
 * cg12345: No kidding. And the Baseball Bat of Awesome makes a welcome reappearance!

Operation Awesome by AND
 * Recommended by Lady Of Procrastination
 * Synopsis: A different sort of Journey's End Fix Fic.
 * Comments: The title says it all, really. Best Journey's End Fix Fic I've read.

Choices by elisi
 * Recommended by Joysweeper
 * Synopsis: Making decisions for others is fraught with problems, even when the intention is pure. In these stories the Doctor tries to give back some measure of control to people whose fates are already sealed. (Sort of fix-its that aren't fix-its. A bit hard to describe.)
 * Comments: Eleven visits Donna and has a talk with River. It's bittersweet - nothing changes, but at least it's their choice, both times.

More Than an Echo by samfeasor
 * Recommended by
 * Synopsis: The continuing adventures of the Doctor's daughter. A creature of first experiences, she is growing and learning exponentially, traveling the universe in the year 6012 (New Byzantine Calendar) and trying to lead the kind of life that would make her father proud: an exemplary one.

Hello Spaceboy and it's equally excellent sequel Rory's Eleventh Hour by roachpatrol
 * Recommended by
 * Synopsis: Doctor!Donna is in the house, which is to say, she never left. How Eleven's series would look with Donna at his side from the very first moments as seen through a series of dialogues and one note. Also known as the story of how Eleven became Amy's alien space dad. Her weird, crazy, idiot space dad.

A Companion's Guide To The Doctor by Chalcedony Rivers
 * Recommended by Kina Kalamari
 * Synopsis: Amy wakes up in the Tardis and, momentarily believing herself to be back on Apalapucia, calls out for a familiar voice. She gets a little more than she bargained for.
 * Comments:

The Effect of Dimensional Transcendence on Mozzarella Cheese by Diane Duane
 * Recommended by: cg12345
 * Synopsis: Five and Nyssa make pizza. Heroic yeast is involved. And there's a recipe at the end!
 * Comments: I simply cannot stress how much better than it sounds this fic is. You need to read this.

Unwritten and Of Blood and Battle by Jecir
 * Recommended by: colaproduct
 * Synopsis: "When you know it's the end, who do you call?" "Your friends, people you trust." An AU take on the Impossible Astronaut/Day of the Moon, with two of the Doctor's oldest friends showing up: Rose Tyler and Captain Jack Harkness. The second fic is a continuation, an AU of A Good Man Goes to War/Let's Kill Hitler.
 * Comments: In addition to the great writing and fantastic "what if" nature of the story, there's the Jack/River pairing that simply works.

Five Minutes and Raising Amelia by Twofer
 * Recommended by: Gomjibar22
 * Synopsis: In "The Eleventh Hour" the 11th doctor takes Amelia with him when he jumps five minutes into the future, five minutes that turn into twelve years. Having accidentally kidnapped her, the Doctor takes her with him on his adventures.
 * Comments: This is a great fic that goes into what would have happen if the Doctor took Amelia with him as a child rather than taking her with him as an adult. There is a large amount of continuity with the previous Doctor Who series with past characters making an appearance and their relationship with the Doctor expounded upon.

It Will Come For Your Children
 * Rec'd by Lady Of Procrastination
 * Synopsis: A combined effort collection of drabbles and ficlets to see how many ways the Doctor can scrounge for new companions from the progeny of the old.
 * Comments: Also check out Folie à Trois, a continuation of Success, which isn't listed.

When A Killer Comes to Play by The Cheater
 * Recommended by oceanlover4evr
 * Synopsis: Someone's out to kill the Doctor for the Silence, and he's taken someone close to the Doctor to draw him out. Between the hit-man and the unexpected hostage, it may just be enough to get the Doctor killed.
 * Comments: I haven't found much when it comes to decent Eleven-Handy fics, but maybe it's because I found this one first. I must say, it is ABSOLUTELY BRILLIANT. It's got great plot, characterization, everything needed for a wonderful story. Definitely a must-read.

Two Months, The Planted Past, and Loop by Sanguine Ink
 * Recommended by Kina Kalamari
 * Synopsis: The Doctor and Rose arrive at Jackie's flat before the ghosts start showing up in Army of Ghosts. Oh, what a difference two months can make. Not just a rewrite of Doomsday - more of a complete reworking.
 * Comments: Yes, it's essentially a Fix Fic to keep Rose from leaving, but it's also so much more. The character voices are brilliant, the humor is so very Doctor Who, and the plot is really well thought out. You do probably have to like Ten/Rose to enjoy it entirely, but it's not overly romantic. The Planted Past and Loop are its sequels, which are just as good as the first, if not better. (Loop is my personal favorite.) A fourth story, Human Nature, is now in the works as well. (If it helps, Jack becomes a main character, and is frankly kind of awesome.)

Regenerations by Jed Rhodes
 * Recommended by seacloudsky
 * Synopsis: The thoughts of the individual Time Lords (and other beings) during their regenerations, and events resembling regenerations, from 1966 to 2008.
 * Comments: Amazing. One of the few fics I have found that shows each regeneration as still being essentually the same person. Regenerations also offers a very interesting explanation for the difference in the appearence of the regeneration process between the Old and New Series. And best yet, it doesn't matter whether you prefer Old Series or New, it's perfectly to cannon.

Crossover Fics
Patchwork/Splintering
 * Crossover with : Quantum Leap
 * Recommended by punksweets
 * Synopsis:Dr. Sam Beckett has been leaping about in time for years; but this time things are different when he crosses paths with another time traveler called The Doctor.
 * Comment's: Well written and the author seems to get all the characters' personalities and quirks down very well.

Outrage by Rich Morris
 * Recommended by Mugen Kagemaru
 * Synopsis: Another crossover piece from the same man that brought us The Ten Doctors. The Sixth Doctor and Mel find themselves involved in a plot while attending a concert with one of Mel's favorite bands: The Holograms.
 * Comments: It's said this portrays the Sixth Doctor in the light he was meant to be shown in, but was denied by the poor scripts of his tenure.

Forever Janette by Rich Morris
 * Recommended by Mugen Kagemaru
 * Synopsis: Two Doctor Who/Forever Knight crossovers in one! In 1348, at a castle in France, the Fifth Doctor and Nyssa of Traken thwarted an experiment by the Master with the assistance of a trio of vampires that happened to be spending the night in the castle. 647 years later, in Toronto, the Eighth Doctor investigates an eerily similar case, and calls on Janette DuCharme and Nicholas Knight, who assisted him in France that fateful evening, to help him track down the culprit. But is it really the Master who is behind these mysterious murders?
 * Comments: Though I have never seen Forever Knight, I have to admit, Rich did a hell of a job on this, I was hooked from the first page. Not to mention the Shyamalan Twist at the end.

Doctor Who/Slenderman Crossover by Anonymous
 * Recommended by Dont Kill Bugs
 * Synopsis: The Doctor fights the Slenderman after Amy catches his attention.
 * Comments: Worth a read just for the sheer novelty of the idea, and for Amy and the Doctor's descriptions of Slendy. The story was written quickly in a 4chan thread (which has since been archived), so there are a few spelling errors, plus the occasional injection by another poster.

Doctor Who: The Manga
 * Recommended by Not Joss Whedon
 * Synopsis: A Crossover into the Kingdom Hearts Saga that includes the Elric Family, Edward, Alphonse, Trisha, Raydia and Timmy among other Crossovers. The Doctor's gonna have quite the Army at Demon's Run
 * Comments: You've gotta try this, you havent lived until you've seen Trisha try her hand at alchemy.

Back to the Doctor by Doctor McFly (crossover with Back to The Future)
 * Recommended by lanky
 * Synopsis: Following the events of the Back to The Future trilogy, Marty McFly thinks that he can finally settle down and get on with his life. Too bad there are creatures in the universe with an interest in time travelers and the energy they emit. On the bright side, sometimes all you need is a good Doctor to step in and save the day.

The Man With No Name by Frostfyre7 (crossover)
 * Has its own Trope Page.
 * Recommended by TEN
 * Synopsis: The Doctor is moping after the events of "Runaway Bride," and his TARDIS decides to snap him out of his funk by dropping him in Alliance Territory. He gets rescued from a bar brawl which was caused by the color of his coat, and off he goes with our favorite crew.
 * Comments: Firefly crossover. No, don't run away yet, I swear it's good!

The Other or: Scenes From a Failed Session by Azremodehar
 * Recommended by Spire Eater
 * Synopsis: Doctor Who/Homestuck. 'Rassilon knew it was coming'. Imagines a possible session played by the Deca during their youth on Gallifrey.
 * Comments: The slightly detached narration is chilling, hitting a tone far bleaker than either Homestuck or Doctor Who normally go for.

Just Impediment by Doyle
 * Recommended by cg12345
 * Synopsis: How the Tenth Doctor became Queen Elizabeth I's enemy. Crossover with Blackadder II, and perfect in either universe.
 * Comments: Now that the author's been shown to be either 1) eerily prescient, or 2) Russell T. Davies in a cunning disguise, I like to think that the incident alleged in "The End of Time Part 1" happened exactly this way.

More Trouble than it's Worth by Settiai
 * Recommended by Trimeta
 * Synopsis: Captain Jack books passage aboard Serenity, but the crew had no idea what they were agreeing to...
 * Comments: Very brief one-shot with excellent character interaction between Jack Harkness and the Firefly cast.

Damage Control by Bookkeeper The
 * Crossover with: Torchwood
 *  Status: Completed, with one completed sequel and a third on the way.
 * Recommended by
 * Synopsis: The Tenth Doctor shows up at the Torchwood Hub after a nasty experience in a testing facility. As it is, this one is only the latest in a long line, and Jack and his team (and Martha) are left to deal with the fallout as the Doctor finally hits his breaking point. Sequel is Inertia. Set after "Voyage of the Damned" for Doctor Who and "Sleeper" for Torchwood.
 * Comments: Pretty genuinely heartbreaking, and incredibly well-written. Not too much plot (although Inertia has an excellent one), but so totally worth reading. The author is an amazing writer.

Like an Onion Inside Out (The Doctor, the Queen, and the TARDIS Remix) by spiralleds
 * Recommended by Looney Toons, Vorticity
 * Crossover with: The Chronicles of Narnia
 * Pairings: The Doctor/Susan Pevensie
 * Status: Complete
 * Synopsis: Susan Pevensie met the Doctor three times in the course of her life -- once in a cemetery, once in her attic, and once after the death of her siblings.  The third time she did not refuse the call -- and her companionship led the Doctor to a place he'd never been before.
 * Comments: A beautiful story with an uplifting ending.  Especially noteworthy for a wonderful idea I've never seen anywhere else -- a notebook stashed away in the Companions' quarters of the TARDIS, entitled The Care and Feeding of your Doctor, containing decades' worth of hand-written observations and advice about the Doctor from those closest to him.

Shipping Fics
Stories focused on the romantic relationships between the cast.

Threads by Vali
 * Recommended by Namta
 * Pairing: Doctor/Romana I
 * Synopsis: Character study of Romana I.
 * Comments: Manages to tie angst, stream-of-consciousness, and really hot snogging into a fairly tightly-plotted part of the show's history, while making everything look completely reasonable.

''[http://community.livejournal.com/andtheropes/1818.html We'll Always Have... You Know]'' by nostalgia_lj
 * Recommended by Micah
 * Pairing: Doctor/Donna
 * Synopsis:
 * Comments: A hilarious Doctor/Donna oneshot, featuring an aggressively clueless version of the Doctor.

Time, Roses, and the Wolf by Amy Wolf
 * Recommended by Katherine
 * Pairing: Doctor/Rose
 * Synopsis: A series of vignettes, in which the Doctor meets Rose in every regeneration.
 * Comments: There are definite shipping elements (he also kisses her in every regeneration), but the story is more appealing for how it characterizes how each of them change and the situations that contrive their meetings.

Trifle by enzymion
 * Recommended by Stare Pris
 * Pairing: Amelia/Rory
 * Synopsis: Christmas 2005. A funny, cute, one-shot.

Facade by wmr (Explicit)
 * Recommended by Sadistic Apathy
 * Pairing: Ten/Rose
 * Synopsis: Set just after The Idiot's Lantern. The sight of a faceless Rose haunts the Doctor, and he seeks her out for reassurance.
 * Comments: Wonderful little ship-fic that manages to mix the usual fluffy/angst with humour, especially in the chapter from Rose's point of view. Good if you're looking for something sweet and in-character.

The Girl on the Horse by orange_crushed
 * Recommended by Ayries
 * Pairing: Ten/Rose, Ten/Reinette sort of mentioned.
 * Synopsis: A short AU to The Girl in the Fireplace, where Rose goes through the mirror rather than the Doctor and spends several weeks battling historical underwear, amongst other things.
 * Comments: Wonderful Rose voice, and everyone involves comes off better than they did in episode IMO- and I say that as a fan of the episode! Turns something heart wrenching into a witty, humorous and yet still slightly bittersweet story without missing a beat.

In Between and All Over Again by Skellerbvvt
 * Recommended By: StudiousJones
 * Pairing: As the author states - 9/Ianto (Way slow burn) Jack/Ianto, waaayhahyhay eventual 10/Ianto''
 * Synopsis: After being abandoned by his team and Jack for a wild goose chase in the Himalayas and the Doctor, respectively, Ianto Jones has to take care of the rift by himself. Looking to refuel after the epic failure of the Time War, the Doctor shows up. The obvious happens. Epic!fic of DOOOOM.
 * Comments: Seriously epic WIP. Slight crossover with Torchwood, as Ianto Jones is a main character and they briefly mention the Hub. Basically, Ianto meets the (Ninth) Doctor before Jack does, but only in the Doctor and Rose's timeline, not his or Jack's. Yeah. . . a big time travel induced headache, but worth it!

The Lonely God by Batman Boxers (Sarah)
 * Recommended By: StudiousJones
 * Pairing: Ten/Gerard Way, past
 * Synopsis: I’m the Doctor,” he said simply, extending his hand for Gerard to shake. Gerard numbly obliged, his face barely masking his confusion. 
 * Comments: Two of my favorite things are now one. Still a WIP as of this post, but amazingly done. Gerard has been living in England since  as an artist. Then he meets the Doctor and his life becomes a hell of a lot more dangerous.

Vita Longa by Sam Storyteller
 * Recommended by: Desiderii
 * Pairing: Rory/Amy/Eleven, slight Jeff/Rory
 * Synopsis: Spoilers for The Big Bang/5.13. Rory's life is a romance, but definitely not the one he expected.
 * Comments: A pretty awesome fic dealing with Rory's situation, all through The Pandorica Opens to after The Big Bang. It's also very accurate to history and the voices are spot on - and the threesome!

Alternatively by
 * Trope page
 * Recommended by: Edgar L Night,
 * Pairing: Ten/Rose, Alt!Ten/Rose
 * Synopsis: Post-Doomsday. "She can't live a fantastic life without him; maybe she doesn't have to." While on an assignment with Torchwood, Rose encounters the Tenth Doctor of Pete's World (whom the author has taken to lovingly calling "Altie").
 * Comments: A beautiful fic, alternately thrilling and simply flufftastic. Side effects may include insomnia and squeeitis.

In This World You Cannot Change by Harold Saxon
 * Recommended by: Jade Eyes 1
 * Pairing: Master/Donna
 * Synopsis: Post "Journey's End", AU. A mind-wiped Donna Noble unwittingly resurrects the Master, who has lost all memory of his past crimes--and his madness. Transported back in time to the start of Harold Saxon's reign of terror, the newly-sane Master and former companion find themselves fighting alongside the resistance during the Year That Never Was.
 * Comments: This story is, without a doubt, the most well-written, intriguing Doctor Who fic I have ever encountered. Expertly plotted and paced, it takes the potential Crack!Fic premise of a Master/Donna pairing and makes it utterly, heart-breakingly believable. The ending is a guaranteed tear-jerker, and one you won't soon forget.

Paradise Lost by unfolded73
 * Recommended by: Purple Bouncy Ball
 * Pairing: Ten/Ten.5/Rose. Slash, het, NSFBS (Not Safe For British Schoolchildren).
 * Synopsis: A retelling of The Stolen Earth/Journey's End, in which Rose is still in this universe and married to the Doctor, with some martial problems stemming from a traumatic wartime experience. Ten.5 (dubbed the other Doctor by this author) enters the picture in the metacrisis, and things get a lot more complicated.

Twelve Cliches That Never Happened To Martha Jones
 * Recommended by peppermintflame
 * Pairing: Martha/Ten
 * Synopsis: It very nearly should be called '12 Times Martha Wanted To Kill The Doctor But Didn't'. It is very, very hilarious. To give a synopsis would be to ruin the beauty of it.
 * Comments: Great for Martha/Ten shippers, and the writer really has captured their voices.

As the Crow Flies by Empatheia
 * Recommended by Crackersdon'tmatter
 * Pairings: House/Doctor.
 * Synopsis: Ten falls literally falls out of the sky and meets Gregory House for it. After that...well...the Q are involved. And bacon with a side of eggs. Oneshot, as it should be.
 * Comments: The polar opposite of comedy

I can't feel my feet and other parts by Empatheia
 * Recommended by calvin2x4
 * Pairings: Amy/Doctor
 * Synopsis: An alternate ending of Amy's Choice, showing what would have happened if Amy had chosen the Doctor over Rory.
 * Comments: For Doctor/Amy shippers.

The Long Way Home _thirty2flavors and goldy_dollar
 * Recommended by flamingpie
 * Pairing: Ten II/Rose, Ten/Rose, Eleven/Rose, Eleven/River
 * Synopsis: "After losing the Doctor, Rose sets off to find him again." Is the summary provided by the authors. To say too much more would really spoil it. I'll just add that it takes a rather cliche plot involving Ten II/Rose and Ten/Rose and turns it wonderfully on its head.
 * Comments: The voices here are all wonderful. Eleven and Amy are a bit off, as this was written prior to series five, but not badly enough to be distracting, and they don't play the largest of parts anyway. It has what is quite possibly the most beautiful conclusion to any fanfic I've read in years.

Chasing the Paradox by nemaline
 * Recommended by kyrilu
 * Pairing: Tenth Doctor/Simm!Master
 * Synopsis: "When the Doctor stumbles into his own future, he takes the chance to find a way to co-exist with an old enemy. But such things are rarely easy, and always come with a price - particularly when the Master is involved."
 * Comments: A very in-character Doctor/Master fic. Be wary of the R rating, though. The timey-wimeyness in this story is well-planned out - make sure to keep in mind the events that occur with the past, present, and future selves!

The Pandora Project by calapine
 * Recommended by kyrilu
 * Pairing: Tenth Doctor/Simm!Master. Rated PG-13.
 * Synopsis: At the end of series three, the Doctor and the Master end up travelling together and totally manage not to destroy each other or the universe. More or less. Meanwhile, Martha gets a job offer from UNIT, Jack fails to realise his team are a bit useless, and there's a giant squid for no good reason whatsoever.
 * Comments: Quite well-written Doctor/Master. A fun read.

One Moment in Time by Brownbug
 * Recommended by Kari910
 * Pairing: Simm!Master/OC/Jack
 * Synopsis: Tejanakaturadilena (Tejana for short) is the Doctor's daughter, born from an arranged marriage between two noble Gallifreyan families and who was still a child in the Academy when her father was forced to leave his home planet. She's travelled off and on with the Doctor and has known the Master all her life. So what if she ended up with the evil Time Lord on Gallifrey on the Last Day of the Time War and they both needed each other to escape? AU
 * Comments: A very well written story, captures your attention and keeps it. three sequels so far, The Portal to Eternity, So Many Things Should Have Been Different, and Return to the Valiant

Feeling Electric by ProfessorSpork
 * Recommended by: greeneyesrock
 * Pairing: Tenth Doctor/Rose Tyler
 * Synopsis: A look at how the Doctor and Rose would've turned out if they were both always human. "She walks into the comic book store, and everything changes. An AU story. / "No!" she insists, but she's grinning and bumping his shoulder and he has never, ever talked to anyone like this before."
 * Comments: Very well written, with many bits of the show woven in through it. Well worth a read.

The Celebrity Exemption by seriousfic
 * Recommended by: Malteaser, Gemmabeta
 * Pairing: Amy/Rory, Jenny/Vastra (Also mentioned: Doctor/Master, and
 * Synopsis: For two thousand years, the Last Centurion stood watch over the Pandorica. Nothing could deter him from his self-imposed duty. Nothing could tempt him away from his lost love. And then Charmed premiered.
 * Comments: This is hilarious: the sounds I was making weren't even human. NSFW towards the end, but my god. You will laugh FOREVER.
 * Seconded, seriously laugh-out-loud funny, and everyone acts surprisingly in character, what's with the loudmouth Amy, and the passive-aggressive Rory and a Doctor sleeping in racecar beds, which just makes it so much funnier (and sweet).

Standing Waves by Christina K
 * Recommended by: Coral542383
 * Pairing: Amy/Rory, River/Doctor
 * Synopsis: Williams was recruited into the Service because he could remember things that hadn't happened yet, and things that were never going to happen.
 * Comments: It's a spot-on character study with focus both on the main subject and people and things around said subject, with heartwarming and heartbreaking moments (some at the same time thanks to, well, Time).

An Incredibly Odd Wedding by Sanguine Ink
 * Recommended by Kina Kalamari
 * Pairing: Ten/Rose
 * Synopsis: Jackie calls Rose to tell her she's getting married. Rose drags the Doctor with her to attend.
 * Comments: Normally, pure fluff fics like this one leave me with a skeptical look on my face and a desire for something less ridiculous, but this one was a fantastic waste of ten minutes. Mostly a humor fic, it had me laughing out loud multiple times, and the whole thing was surprisingly believable, considering.

That Home I Find Outside Your Door by Queen of the Castle
 * Recommended by Jackdaw
 * Pairing: Ten/Rose AU
 * Synopsis: There are lifetimes' worth of grand adventures, incredible far-off places and endless running for his life stored away inside his head. She's just not sure how much of it is his.
 * Comments: A 17k AU in which Rose has never left London and is still just a shop girl, and it had me sniffling and grinning and reading it over and over again. Even if Rose is not usually your cup of tea, this story takes a new perspective on her and her relationship with the Doctor, and it's very much worth your time.

Fan Vid
Doctor Who Anime by Otaking 77077
 * Reccomended by Speedball
 * Not a fanfic, but a fan-movie, animated with loving care and (mostly) voiced by audio clips of existing Doctor Who footage (suppling new voices as necessary)
 * Synopsis: Now finished with roughly 11 minutes of footage as a mock trailer for a whole fictive anime season. The "plot" consists of Davros and the Daleks struggling with the Master (Two of them!) and the Cybermen over control of Japan while the Third Doctor arrives and meets the typical anime Action Girl for a companion. A number of spiffy action scenes are shown, including the Brigadier doing a Worf Barrage on a Cyberman ship and a Five Rounds Rapid by some American soldiers on a squad of Daleks. There are furthermore cameos of Sutekh the Destroyer, the Sontaran Battlefleet and the Supreme Dalek. It also stars professional voice actors Sachika Souno and Phillip Sacramento.
 * Unfortunately, as of June 6, 2011, the entire thing was removed from YouTube. But fear not! Here's a video file before it was removed.
 * Luckily someone else has reuploaded it.

The Ten Doctors by BabelColour.
 * Recommended by Kipperonthefloor
 * Also not a Fanfic but a series of videos made using well edited existing footage and audio from both Who and Non-Who sources to make a new story. Three videos so far but the story isn't over.
 * Synopsis: The Doctor's first and second incarnations have been removed from the time stream so the lord president of Gallifrey enlists the help of the Doctor's third to tenth incarnations to save himself and the history of the Universe, but everything is not what it seems.

What About Everything - What About Babelcolour by BabelColour.
 * Recommended by: seacloudsky
 * Considering that music videos are being added, this needs to be here.
 * Synopsis: All the doctors (1-11) are shown in the vid to the song What About Everything. Babel Colour has used his usual editing to not only shift through thousands of clips, but bring them together so that they completely match the lyrics and rhythm. The seamless blending of the title sequences is simply amazing, and makes me proud to be a Doctor Who fan.

I Owned the Stage // Doctor Who by Liisakee
 * Recommended by: Illuminated Darkness
 * Beautiful editing, beautiful quotes, beautiful music, and my favorite video by far.
 * Synopsis: A video set to Hoppípolla by Liisakee that perfectly sums up Doctor Who.

The Hitchhiker's Guide to the Daleks by Andrew Orton
 * Recommended by: cg12345
 * Synopsis: "The Hitchhiker's Guide to the Galaxy has this to say about Daleks..."
 * Comments: An absolutely spot-on recreation of one of the animated Guidebook sequences from the old TV series, with perfect Adams-esque dry wit.

Tenth Doctor : The Musical by di0br.
 * Recommended by Nadilune
 * If you're one of the few people in fandom who hasn't seen this yet, go watch it. Just go. This is one of the best things I've ever seen : funny, a genius idea, and a wonderful tribute to Ten.
 * Synopsis: A summary of the Tenth Doctor's run in 7 minutes and 20 songs.

His Name is the Doctor by seduff.
 * Recommended by Nadilune
 * Wonderful editing with perfect voiceovers. Just epic. Nine and Ten shine in this.
 * Synopsis: A tribute to the Russell T Davies Era. His friends and companions talk about their Doctor...

Eleven is Cool by humansrsuperior.
 * Recommended by Nadilune
 * This vid is pure joy. It perfectly shows this incarnation of the Doctor's personality : dorky, flaily, fun.
 * Synopsis: The Doctor is cool. An Eleven appreciation vid

Geronimo by KatrinDepp.
 * Recommended by Nadilune
 * Another vid about Eleven. Lighthearted, fun, with a catchy and appropriately-titled song. Just watch it, you won't stop smiling.
 * Synopsis: The Doctor antics in series 5 and 6.

Glósóli by such_heights.
 * Recommended by Nadilune
 * Gorgeous. A layered, meta-driven view on series 5 and 6. It's amazing, epic, thoughful, and has the Ponds being their adorable selves.
 * Synopsis: "That's a fairytale." "Aren't we all?"

The Adventure by Calapine.
 * Recommended by Nadilune
 * This one involves all the eleven Doctors and their companions, and it's truly magnificent. Definitely worth a look or three.
 * Synopsis: A nice trip through time and space.