These are all one-parters. All are under 3000 words; most are 1000-2000.
For a few of these, I couldn't find the LJ entries, so the links go to Teaspoon instead.
The Doctor (general)
So You Want to Be a Time Traveller: A Brief Introductory Guide for the Time Lord's Companion - The Doctor lays it out for a (hypothetical) new companion. (Could be any Doctor, but at the time of writing, I was thinking of Ten. This was after Journey's End, but before the announcement of David Tennant's departure, so I thought he might get at least one more regular companion before he was through.)
The Sum of His Parts - A newly-regenerated Eleven wonders who he'll be this time. (Not actually an Eleven story at all. At the time, Ten's regeneration seemed comfortably far in the future. Of course, at the end of the same month that I wrote it, DT said he was going. D'oh! Anyway, this is really just a summing up of the first ten Doctors.)
Nine
Moment - A drabble. The Doctor reflects on the turn his life took when he met Rose.
Ten
Bad Timing - The Doctor's thoughts at the end of The Stolen Earth.
Kiss and Run - The Doctor had more onscreen kisses in his tenth incarnation than all his previous selves put together. What did he make of them?
Love the Running - The Tenth Doctor's reasons for trying to escape his destiny. (Spoilers for The End of Time Part One)
Phoenix - He feels the fire gathering.
Show Me the Stars - The Doctor's thoughts at the end of Planet of the Dead.
Too Far - The Doctor's thoughts toward the end of The Waters of Mars.
Ten and Donna
Aftershock - After the events of 1926, the subject of a certain method of detox comes up. (Spoilers for The Unicorn and the Wasp)
Crimes of Fashion - The Doctor's sartorial past comes back to haunt him.
Echoes - Donna and the Doctor contemplate what happened on Messaline. (Spoilers for The Doctor's Daughter)
From the Ashes - Donna struggles with the aftermath of the eruption of Vesuvius. The Doctor helps in his own inimitable fashion. (Spoilers for The Fires of Pompeii)
A Funny Old Life - "It's a funny old life in the TARDIS." - Partners in Crime. Donna thinks about how traveling with the Doctor has changed her. (Companion piece: Someone to Stop You, below. Both stand alone.)
Last Call - Donna really shouldn't have eaten all that fruit.
Moving Through Shadow - The Doctor and Donna attempt to come to terms with what happened on Midnight.
The Purple... Thing - Donna finds a thing. It's purple.
Secret Santa - Donna never does learn who keeps sending her anonymous gifts every Christmas.
Someone to Stop You - The Doctor's thoughts about Donna. (Companion piece: A Funny Old Life, above. Both stand alone.)
Spaceman - Donna finds the perfect gift for the Time Lord who has everything, and nothing. (Spoilers for Silence in the Library/Forest of the Dead and The End of Time Part Two)
To Absent Friends - She'd known she wasn't the first, but she hadn't known there'd been quite so many. (My first completed fic in the fandom. You know how first fics always seem dorky as hell to you when you go back and look at them? This? No exception.)
Truth or Consequences - When she and the Doctor get themselves locked up -- again -- Donna sees an opportunity.
What's in a Name? - Donna asks the Doctor a question he can't answer.
Ten and Martha
Holding a Sun - Martha reflects on her relationship with the Doctor.
Like So - The thoughts of Martha and the Doctor at the end of Smith and Jones.
Unfinished Business - Martha and the Doctor dance at her wedding reception. Things are said. Closure is had. (Slightly jossed by The End of Time Part Two, but oh well.)
Ten and Rose
A New Face On Things - The Doctor finally gets to check himself out in the mirror for the first time since regenerating, explains a few things to Rose about his change, and worries that their relationship might not survive it.
Ten and Sarah Jane
The Biggest Family on Earth - The Doctor's companions living on Earth get together for Christmas Eve.
A Tough Act to Follow - Sarah Jane Smith's thoughts and feelings as she encounters the Tenth Doctor. (Spoilers for School Reunion)
Whatever It Is - The morning after the night before. Talking, making love, more talking. Takes place soon after Planet of the Dead, but before The Wedding of Sarah Jane Smith. (My only NC-17 Who fic so far. I'm a gen writer and a non-shipper, so I have no idea what put this in my head.)
Ten and River
Not One Line - His first meeting with her is her last with him. River Song's thoughts in the Library. (Spoilers for Silence in the Library/Forest of the Dead)
Ten and the TARDIS
His Ship - The TARDIS does what she can. (Spoilers for Journey's End)
Sarah Jane
A Taste of That Splendor - Sarah Jane's last dream. (Character death) - A ficlet written in tribute to Elisabeth Sladen.