Mostly these were written in reaction to the Girl in the Fireplace episode and all the kerfuffle it's caused with the shippers/chippers/people who just like the show for the show's sake... So here be spoilers.
The Short Revolution of Time by
nostalgia_lj - Alternate ending to the episode and the implications thereof. Gorgeous writing, breathtakingly heartbreaking (can I use more flowery language?). Just go - read. :)
Equals by
mythverdandi - I already recced this on my own journal and whole-heartedly do so again here. A post-episode fic which is kinda lovely (albeit a little heavy on the writer's OTP...)
Couers, pluriels by Neth Dugan - again, already recced on my own journal and again, whole-heartedly repeat the rec. Reaction/POV/Stream of consciousness that just nails the characters perfectly..