There's a meme been going round recently getting you to list the top 10 of your fics by popularity. (I saw it initially on morganstuart's LJ, though it now seems to have vanished from there, and AJ Hall has also done it).
Since AO3 has most of my fics on it and hit counters, I've used that. The one fic that isn't on there that might perhaps come in the top 10 otherwise is Last letter, which I wrote early on in fandom and now seems embarrassingly sentimental, but still sometimes get found or even recced).
I've also, just for comparison, put in my bottom 5 fics.
My most popular fics on Archive of Our Own (hits as at 10/5/12, excluding fics posted in that week and non-Sherlock fics)
1) Jealous Guy (9000 words, mature) Kudos 131, Hits 3901
Mystrade: Lestrade suspects Mycroft of cheating on him.
2) Impure Genius (22,000 words, mature) Kudos 151, Hits 3539
Sherlock/John: Insecure, self-harming Sherlock being sorted out by John via a boot camp and sex.
3) SNAFU (18,000 words, mature) Kudos 113, Hits 2947
Sherlock/John: John attempting to be normal and failing badly, despite Clara's help.
4) Tastes (3,000 words, teenage) Kudos 49, Hits 2723
Mycroft/John: Sherlock gets jealous about John's personal life (First part of Blame Jeremy Bentham series).
5) MI Sex (9,000 words, explicit) Kudos 183, Hits 2721
Mystrade: Lestrade discovers Mycroft's murky past in the Secret Service.
6) Half a loaf (20,000 words, explicit) Kudos 126, Hits 2460
Mycroft/John: Straight John gradually falls for gay Mycroft and they finally get together.
7) Goodbye, Irene (2,000 words, teenage) Kudos 117, Hits 2333
Gen: My alternative ending for Scandal in Belgravia, in which Irene outplays Sherlock.
8) Baker Street Imp (16,000 words, general audiences) Kudos 93, Hits 2297
Sherlock/John: Sherlock and John have to look after Clara's seven-year-old niece.
9) Holmes comforts (12,000 words, mature) Kudos 56, Hits 2086
Mycroft/John: Mycroft trying to get together with John without letting Sherlock know (Second part of Blame Jeremy Bentham series).
10) Sex doesn't alarm me (221 words, mature) Kudos 51, Hits 1884
Mystrade: Crack fic where Sherlock discovers worrying pictures on Lestrade's phone
Bottom 5 on AO3
1) Poor Jenny, bright as a penny (1,800 words, teenage) Kudos 8, Hits 74
Femslash: The Pink Lady's backstory.
2) Calm and Storm (442 words, mature) Kudos 6, Hits 75
Ella/Sally: 221Bs in bed
3) Straight, Smooth, Scholar (663 words, general audiences) Kudos 2, Hits 80
Ella/Sally: getting to know one another
4) Patterns (3,300 words, mature) Kudos 7, Hits 103
Sally/Harry meet and connect
5) Six hours, forty-six minutes (2,200, mature) Kudos 8, Hits 106
Ella/Anthea: Anthea has a bad day: Ella helps her unwind.
The bottom five are hardly surprising: femslash doesn't tend to get that many readers, though the people who do read it often like it a lot. The top ten are more surprising: my readers mostly want slash, but not necessarily Sherlock/John. I'm particularly surprised that several of my Mycroft/John stories rate so highly, but that may be because not many people write that pairing. And I also know several of them have been included on rec lists by M/J shippers.
More generally, what my readers seem to want is long, angsty fics. "Impure genius", "Half a loaf" and "SNAFU" are among the five longest individual fics I've written, and "Baker Street Imp" and the "Blame Jeremy Bentham" sequence are also very long. I've written around fifty 221Bs, but only one of them makes it in the top 10, and it may well get overtaken long term by "You cannot libel the dead" in 11th place. "Sex doesn't alarm me" is also the only purely comic piece in the top 10, though "Baker Street Imp" is also pretty fluffy, and "Goodbye, Irene" is largely angst-free. Otherwise, it's reticent male suffering FTW, though all the top 10 do eventually have happy endings.
There are several other longish Mystrade fics in positions 11-20, but there are also a few other fics of mine which are similar to these popular ones and yet are much further down the list. For example, The Penultimate Problem, which I think is one of my most ingenious long Mystrade fics, and with bucketloads of angst, hasn't done very well. And I'm also disappointed at the showing for Doctor meets Doctor; I suspect that doesn't get many readers because nobody but me ships John Watson/Mike Stamford, but I still think it works well as a combination of unlikely romance and excessive angst. (As well as having the only (two-person) sex scene I've ever written that is het and slash simultaneously).
It's interesting seeing these details of my readership, but it's not particularly going to change what I actually write. There will be more femslash up soon (including more long, angsty femslash, which in the ratio to time spent writing versus readership is really not effective). There isn't likely to be any more Mycroft/John for a long time, because Series 2 John and Mycroft don't seem to me to be a viable partnership. And too many of my stories at the moment I can't think of a happy ending for. But then if you prefer people who do exactly the things you like, you wouldn't be a Sherlock fan anyway, would you?