My recs are predominantly New Who this time, with some crossovers - and I should probably mention that I don't count stories merging Dr. Who, Torchwood, and/or The Sarah-Jane Adventures, or different eras, as crossovers; to me they're all part of the same wibbly-wobbly timey-wimey universe.
Starting with something brand new:
Story: In Her Absence
Word Count: 71047
Author's Summary: A tale of the early days of the Silurian warrior Madame Vastra, ranging from her early travels with the Doctor to her adventures in the alleys of Victorian London.
Characters/Pairings: Jenny Flint, Madame Vastra, Other Character(s), The Doctor (11th)
Recced because: I'm a big fan of Madame Vastra and Jenny, and would love to see them in a spinoff series, but there are relatively few stories about their early relationship, and I can't think of any that cover Vastra's initial meeting with the Doctor and the beginning of her career in Victorian London. This covers all of that, adding in an explanation of her use of Japanese swords, an alien encounter, a mysterious menace, and lots of other fun stuff. It was posted to the lizardladylove community just days ago, and I knew as soon as I read it that it would be one of my recs. Incidentally, there are some author's notes for the story here: http://lizardladylove.livejournal.com/28726.html
There was an incursion one mile from her current position, near Forward Stasis Chamber Viridian Alpha. Closest to the surface, the warriors there would be the first line of defense in the event that their cavern was breached. Concerned that they too had somehow not survived their hibernation, she took off at a run to survey the situation and drive off any possible invaders. She knew she was alone, but she reasoned it was most likely that any invaders would be simple, primitive apes. She could certainly handle a group of them on her own.
The tunnels grew lighter as she closed in on the surface. There was a sharp bend before the final incline toward the stasis chambers and the outside. She paused there, slowly peering around the corner to assess the situation.
Some two hundred or three hundred yards ahead, what appeared to be a group of apes stood, as he expected. She did not expect them to be wearing hat appeared to be clothes, nor did she expect them to be carrying flame or what appeared to be digging tools. She wondered for the first time how long she had been asleep, as these apes had none of the heavy, wiry hair that covered their bodies as last she saw, when she and her sisters hunted them for sport. They chattered and chattered at each other, but their sounds had the actual shape and form of words.