The Adventures of the Doctor and Rory the Roman by jesterlady
"Rory's waiting for 2,000 years. How many Doctors do you think he'd meet in that time?" Pretty much all of them, really.
Aftermath by Woof
Post-PotW; on regeneration, reunions and coping. Slightly fluffy, slightly angsty, it just about hits the spot.
the air that i breathe by seren_ccd
Short-but-lovely Alec/Emma, after the Doctor blows through their life.
All in a Day's Work by miss_baxter
[Doctor Who/Hitchiker's Guide to the Galaxy]
Donna Noble has to save the world from the Vogons. Screamingly funny fusion of the two universes, told with a dead-pan HGttG voice.
The Candle That Burns Brightest by icebluenothing
Rose took the long way around at the end of "Parting of the Ways"... A really cool AU of Rose returning to normal life when she's not normal anymore. Strong and heartbreaking.
The Care and Feeding of Tiny Humans (and slightly larger Time Lords) by Netgirl_y2k
"The one where the Doctor comes back for little Amelia Pond." Oh, how I wish it was longer; I always wanted this story.
The Christmas Variation by surrexi
"Jack wakes up just a tiny bit quicker at the Game Station, in time to witness the Doctor save Rose's life and to board the TARDIS with them when they leave. How will Jack's presence change the events that follow the Doctor's regeneration and the trio's subsequent arrival in London just before the Sycorax invasion?" Love this.
Close Encounters of the Team TARDIS Kind by wnnb_darklord
A genius AU, in which Rory meets up with Ten and Donna long before the adult Amy joins up with Eleven. The voices are gleefully perfect.
Courting Gloriana by hathy_col
A great mix of history and fun, as the Terrible Trio crashes a party for Her Majesty Elizabeth I. Rose and the Ninth Doctor watch and kibbitz; Jack dances, flirts, and tries not to get married. Lots of actor in-jokes, and a deft touch with both the history and the comedy.
excerpted from The Adventure of the Plum-Colored Glow, the Potato, and the Really Good Chocolates (Book 3 in the Madcap Adventures of Amelia Pond, age 7, Time Traveler) by belmanoir
Funny and perfectly young!Amelia, an au I think we would all like to have seen.KikiRec
Father's Day by SnubNosedSilhouette
"'Do-' Rory seemed to reconsider, then barreled ahead with his question. 'This is a silly question, but, do you have a dad, River?'" Explorations of neglected relationships: River and Rory, and River and Brian.
Five Times Jack Harkness Never Interfered With Rose Tyler's Timeline (and One Time That He Did) by travels_in_time
Pretty much just what the title says; Jack in London, watching Rose grow up. KikiRec
Gingerbread by thirty2flavors
Rose and human!Ten meet the alt!Donna. Which doesn't even begin to cover the sheer hilarious awesomeness of it all. There's a much longer sequel, Revolution, and a few more before and after that.
here (in your arms) by such_heights
In an attempt to make Rory feel appreciated, The Doctor and Amy accidentally get into a hugging contest. Sweet without being overly so, and altogether lovely.
here's to all the boys who came along by Lirazel
Lovely Rory introspection.
The Idiot's Guide to Foiling Alien Invastions by Netgirl_y2k
"Jackie and Mickey save the day by bickering, drinking lots of tea and spending a lot of time in the pub in the middle of the day." Another one where I want to forcibly insert periods, but it's too giggly for me to really get that worked up. Featuring Sarah Jane and UNIT, among others.
In Motion by pocketmouse
Part of the "I Saw Three Ships" challenge, so you can guess it's something of an Eleven/Amy/Rory precursor, but it's also a gorgeous story interweaving an exhausted and injured train ride through Siberia with some of Amy and Rory's time on the Tardis.
Just Rory by philote_auctor
"Wherein Rory is a perfectly competent nurse and the Doctor makes a lousy patient." Beautiful Rory POV, lovely Amy/Rory moments.
Living History by MinervaFan
Sarah Jane and the children are entrusted with a priceless legacy.
Look Upon This Sky by Cadhla
Rose wakes up the morning after she joins the Doctor, and learns more about what she's gotten herself into. A really nice rumination on the Companions and their legacy, done with poetry and style. Cadhla continues the lovely theme with What Does the Sky Reply and Terminus of Prayer (spoilers for PotW).
Pawns in the Game by surrexi
This is the Ten/Rose/Jack reunion story I always wanted and never got. But here it is, along with an equally satisfying sequel. These stories make me happy.
The Pond Continuum by kaydeefalls
"Five people who have never heard of the Ponds (but might have met them anyway), and one who has." A fun ride through familiar faces and episodes. KikiRec
Relatives and Relativity by Emeraldwoman
Nine, immediately post-regeneration, and two sisters remind him what he still has to live for. Beautifully done, but what else do you expect of Yahtzee? Sense & Sensibility crossover.
Rory's Eleventh Hour by roachpatrol
"'Oh god,' Rory moans, still giggling weakly. 'I'm trapped in a haunted house with a dead girl and her alien space boyfriend and we are going to be eaten by a giant crazy alien space eel. This is the worst day ever.' 'He's not my boyfriend,' Amy says." Short and funny au.
River Song and the Lost Tomb of Ardun by nancybrown
River's professor for her first archaeology class was a self-declared expert on late twentieth and early twenty-first century Earth history. Naturally, she hated his guts. [KikiRec: Sooo much twisty timey-wimey fun- and I didn't see several of the surprises coming.]
Stealing Time by such_heights
Probably my favorite of the post-Angels Take Manhattan fix-it fics.
Snow White Lies by Tara O'Shea
Fairy tales continue past happily ever after -- a beautiful look back and forward at Nancy.
Sojourn by saganamidreams
A stark, sometimes painful look through Jack's eyes at his first days on the TARDIS; happy bunnies are in short supply, but the characterization rings quite true, tracing the transition from solitary conman and outsider to trusted friend and comrade. Quite well done, and definitely not in the usual mode of Jackfic.
Steal Me Away by themonkeycabal
A wonderful, wonderful Jack/Doctor/Rose reunion fic; everything you ever wanted for the terrible trio, I promise, executed with a lovely Jack POV.
Think of Something by Lightgetsin
Nine, right after the war, traumatized and alone. Then he runs into Jack Harkness, an old friend he hasn't met yet. Gorgeous language and a terrifingly perfect glimpse into the Doctor's mind before he started recovering from the Time War.
Time Is Out of Joint by jesterlady
"Rory has lived many lives and their memories clash and splinter and flow into one another and it can be very hard to remember who he really is." I love fics that address Rory's centuries of memories, and this is a good one.
Torchwood Babiez by spastasmagoria
Completely hilarious graphic novel starring the Torchwood (and Doctor Who) Babiez! Yes, there's an explanation (sort of), but mostly, it's a gloriously fun, beautifully illustrated romp.
Where Ever I May Roam by irenak
Silly dialogue-fic of phone calls and text messages between the Doctor, Martha and half the population of Cardiff. KikiRec
The Weight of Us by dollsome
Absolutely brilliant and heartbreaking filler between going home, and crop circles.