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/
( A small sample )