him in the clouds
Jenny goes looking for her father.
Master/Jenny, Master/Doctor, rated R for disturbing themes. Set after 4x06 "The Doctor's Daughter".

A Moment's Grace
On the eve of her return to England, a weary Martha Jones meets an old friend for the first time.
Two/Martha, implied Martha/Sally Sparrow, set just before 3x13 "Last of the Time Lords".

(See fanart for this story, by Infiniteviking.)

Ten Things That Are Almost Absolutely True About Martha Jones, and One Thing That's True About the Doctor
But then Martha takes up with the Doctor, which is practically the same thing, only a million times worse.
Martha, Tenth Doctor, Francine, Jack, Ianto, spoilers through series three.

A Mutual Understanding
"Doctor," says Romana, "I have a feeling."
Four/Romana II, any time, any place.

Providence
Not all the monsters in the TARDIS are locked safely in the attic.
Ten, Martha, Ace, the Brother, set after 3x09 "Family of Blood".

with her own wings
Martha was once the Doctor's maid. Now the Doctor seems to have become Martha's secretary.
Ten/Martha, Francine, Tish, Vicky, post 3x13, "Last of the Time Lords."

Dead Worlds
Lucy Saxon lives in the TARDIS now, and finds that one mad alien is much like another.
Ten, Lucy Saxon, post 3x13, "Last of the Time Lords."

tea time terror for time tots
The Doctor writes an instructive book for children.
Seven

ceremony for the living
The Doctor attends his own funeral.
Seven, Ace, sort of set during Love and War by Paul Cornell, but really could take place any time after Survival.

in a dim light
Romana is a slave of the Daleks, and the Doctor is a nightmare incarnate.
Four/Romana II, spoiler for the Big Finish audio The Apocalypse Element.