By canon, then order of publication. Probably missing some Tumblr fic.
Shopping & Coffee, Tony/Pepper, hints of Pepper/Natasha
Infiltration, Steve/Peggy, Bucky
Unexpected, Steve/Peggy, Natasha
Down and Out on the Red Carpet, Steve Rogers, Natasha Romanoff, Nick Fury, Tony/Pepper, Jane/Thor
Not the Strangest Thing I've Ever Seen, The Avengers fight a dragon
Wide Open Seas, Cinders/Tobias
The Compact, Cinders/Tobias, The Fairy
Dancing in the Library, Sophia/The Prince
One Last Drink, Alistair, Sten
Good Clean Fun, Bethany and Carver, Warden Twins AU
The Kissing Part, Alistair/Sereda Aeducan
Fatherhood, Alistair, Anora, the Old God Baby
Justify the Means, Dwarf-centric AU Blight fic
Security Breach, Isabela/f!Cousland
The Leaving, Merrill/m!Mahariel
Business and Pleasure, Alistair/Anora
Visitations, Morrigan and Flemeth
To Clear the Air, Isabela/f!Hawke, ish
Living Dead Girl, Bethany and Sigrun
Honesty Hour, metafic for "Justify the Means"
Adjustments, Alistair/Elissa Cousland
Storms, Alistair/Sereda Aeducan
Distant Early Warning, Sereda Aeducan, Duncan
After the Fall, Alistair/f!Mahariel
Day in the Sun, Carver/Merrill
Snapshots in Song, Alistair/Sereda Aeducan
Ode to Power, Anora/Alistair
Matters of Trust, Bethany/Keran
In Memoriam, Alistair/Moira Cousland
The Midnight Patrol, Fenris/Bethany
Final Blow, Sereda Aeducan/Alistair
True Stories, Sigrun and Velanna
Destiny, Loral Mahariel, Merrill
Secrets and Lies, Duncan
Water and Waves, Fenris/Isabela
Barefoot in the Snow, Fenris/f!Hawke
Final Fantasy X/X-2
Defender of the Faith, Auron, AU
Doubts, Braska and Yuna
On the Sidelines, Paine and Lulu
Past, Present, Future Tense, Paine/Nooj
Final Fantasy XII
On the Last Day, Ashe/Basch (written for the 2012 Kiss Battle but not posted to AO3 until February 2013)
Distractions, Ashe/Balthier, Fran
Dreams and Obligations, Ashe/Basch
Freedom of the Press, Al-Cid/Ashe(/Balthier)
Engagement, Ashe/Balthier AU
Final Fantasy XIII
Morning Watch, Fang/Vanille
BBC Sherlock: Telephone, Greg Lestrade
Fringe: Chosen, Peter Bishop and Astrid Farnsworth
Welcome to Night Vale: Intern Return, Cecil and Dana
The Tricks of Navigation, Balthier and Tony Stark
An Unlikely Partnership, Sherlock Holmes/Iron Man crossover
On Summoning, Yuna and Fenris
In a Gaming Mood, Jane/Thor, Isabela
Football Hero, Alistair/Steve Rogers, Yuna
Questions and Answers
What pairing/genre/fandom did you write that you would never have predicted in January? I think the Sherlock Holmes/Iron Man crossover tops that particular list. Particularly since it didn't really come from a prompt, but from inside my own head.
What's your own favorite story of the year? Not the most popular, but the one that makes you happiest? "Justify the Means" is a strong candidate. So is "Infiltration". Also my cracky crossover stories ("Tricks of Navigation", "In a Gaming Mood", and "Football Hero") just tickle me to pieces.
Did you take any writing risks this year? What did you learn from them? You know, I'm not sure I really did. Signing up for a challenge -- the MediAvengers mini-bang -- in a large fandom I haven't participated in much otherwise might qualify. But I've accepted that I'm officially multifannish for a couple of years now.
Do you have any fanfic or profic goals for the New Year? I'll write them up in a separate post, either later today or sometimes tomorrow.
From my past year of writing, what was...
My best story of this year: I don't usually like to pick this for myself, but this year I have a clear answer: "Justify the Means".
My most popular story of this year: Of the stories posted this year, the story with the most hits and kudos by far is "Down and Out on the Red Carpet". Not a surprise, even though I posted it only two weeks ago, because it's in a big fandom and has also gotten a lot of visibility through the MediAvengers blog. I'd have been surprised by anything else. Second place in hits is "Temptations", and in kudos it's "Intern Return".
Story of mine most under-appreciated by the universe, in my opinion: The Paine/Nooj stories. I wrote two and updated and reposted an older one, and all passed with hardly a ripple. It's never been a popular pairing by any definition, but most of my old built-in audience for them is gone, and new people haven't really come along to take their place. It's a bit sad and a bit discouraging. On the other hand, maybe these newer stories just aren't as good as the old ones. Maybe I've said most of what I have to say about Paine and Nooj. That thought makes me sad, too. Possibly the upcoming HD re-release will help, both with my inspiration and my potential audience.
Most fun story to write: Writing for the 15 characters meme, which I took prompts for twice this year, is always a lot of fun. Of the more serious stories, I think probably "Justify the Means" is the winner here, too.
Story with the single sexiest moment: "Invitation" was pure porn, almost beginning to end, and I was really pleased with it.
Story that shifted my own perceptions of the characters: I got a much stronger handle on Anora by writing "Ode to Power", as well as Alistair in the king role.
Hardest story to write: "Ode to Power". I'm pleased with the end result, but it went much more slowly than I thought it was going to. I also had several false starts on "Later" and "Water and Waves".
Biggest Disappointment: Missing my wordcount goal for getyourwordsout. I'll have more to say about that when I do my writing goals wrap-up post.
Biggest Surprise: trope_bingo. I've never signed up for that kind of community before, and I've had a lot of fun with it.
Most Unintentionally Telling Story: I'm not sure I have one of those this year.
In conclusion: There are way more stories on this list than I would have expected. This was a year for shortfic -- the only story on this list to top 10k words, "Justify the Means", was almost entirely drafted in 2012, and only three others more than 5k words. I think it's a combination of the kinds of challenges I've been doing (Tumblr prompts and bingo cards, which reward writing more shorter stories), and the fact that I got dropped with a couple of big life distractions this summer (sick cat and back injury). More about what it all means, and my plans going forward, when I do my writing goals wrap-up.
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