Fanfictions that are awesome. You should read them.
This is my favorites list. And seriously, if you haven't read them all ready you should. I finally broke down and categorized them, so you've got at least SOME idea of what you're getting into, besides if it's a series or NSFW. I also updated this list, so it's significantly larger, because there are so many awesome authors out there. :D Enjoy!
Ten/Rose Nine/Rose
Some Slightly Unusual Mistakes Always Wanted
*Series *NSFW
*NSFW
Practical Mythology
Falling Home
*NSFW The Mettle of Merlin
A Sort of Fairy Tale Torchwood Babiez
*humor
Writings on the Wall
Bad Wolf Stories
*Series
Nine/Rose AU
Worthy of Her
I'm Not Really a Waitress
Wild Ride
*NSFW Never Quite Normal
*NSFW
When it Just Happens
Vote Saxon
*Rose meets the Master Nine/Rose AU episode rewrites
Tumbling In Human Hands
The Silver Dollar Paradigm A Man who wasn't There
*Series
Petals
*NSFW
Ordinary
Nine/Rose Crossovers
On Knights and Shining Armor
Sherlock Holmes and the Adventure of the Blue Box
Lover's Tiff?
So We Sailed on to the Sun
Love and the Stuff of Legends
*Series Out of Joint
*NSFW And its folow-up fic: On the Rim
From the Outside Looking In More Things in Heaven and Earth
Family Matters
*Features Susan Foreman
AU Nine/Rose in Pete's World
I Miss my Mind the Most
Illyria
I Will not Fuck the Teacher *Series
*NSFW
A Fable that will Never End
But Broken Lights Eleven/Rose
Epitaph for Fire and Flower Splinter
Effigermus
*NSFW
Canis Lupis
*Series Multi-Era
Falling Slowly'verse Coaster Castles (And Other Sturdy Defenses)
*Series *NSFW
*NSFW
Songs of Innocence and Experience
The Hedgehog Concept
*Series Past, Present, and Future
*NSFW *Series
*NSFW
Master and Commander
*Series Non-Linear Lovestory
*NSFW
The Process of Becoming
*Series Rounded with a Sleep
*NSFW *NSFW
The Awakening Luminescence
Chaos 'Verse A Doctor Lost, a Doctor Found
*Series
*NSFW Moments in Darkness
*Series
*NSFW
Ten/Rose Reunion
Journeys in the In-Between
Deus Ex Machina *Series
*NSFW
Of the Universe
*Series
*NSFW
Twist of Fate
A Papier Mache Mestopheles
Never Was Graceful
A Tale of Two Doctors
She Came with the Rain
Aphelion
Speedbumps on the Way to Forever
*NSFW
Gift'verse
*Series
Journey of a Thousand Miles
Life After
Choices We Made Series
*Series
A Twist in Time
And its follow-up fic: Orbiting Home
Surrounded by Morons
And its follow-up fic: Evil Cupcakes
Ten/Rose AU
Dystopianverse
*NSFW
*Series
Teacups and Lingering Love
Going My Way
The Zepplins'verse
*NSFW
*Series
Bodyguard
The Ringmaster in a Blue Tux, and the Girl with Really Strong Toes
Ten Crossovers
Scheherazade
More Powerful Than Facts
The Engineer's Gift
Ulysses
The Man with No Name
A Little Bit Off
Chance Meetings
The L-Space Trilogy
*Series
*Begins with 9th Doctor
Ten/Rose AU episode rewrites
Don't Blink
The Art of Being Human
And its follow-up fic: Better Days
Smith and Tyler
Ten II and Rose in Pete's World
Failings of Language and Other Technicalities
*Series
The Noble Verse
*Series
Revisions which a Minute will Reverse
We Came to Learn the Sea
Behind Closed Doors
*NSFW
AU Ten/Rose in Pete's World
Alternatively