I have a handful of stand-alone stories that are either set in the same continuity as each other or thematically related in some way.  Here are the collections:

Twilight Holmes

These stories are set in the Twilight Holmes continuity.  Here they are in chronological order:

It's Elementary, My Dear Rainbow

Twilight Holmes: Sabotage After Sunset

Variety is the Spice of Life Challenge

A shipping challenge of epic proportions, which I am going to play in hard-mode: all fifteen prompts, all fifteen ships.

Twidash: Little Wonders (Prompt: A Kiss)

Appledash: The Great Cider Heist (Prompt: An Anniversary)

Raridash: (Prompt: A Gift)

Flutterdash: (Prompt: An Apology)

Pinkidash: (Prompt: A Game)

Twijack:

Raritwi:

Twishy:

Twipie:

Rarijack:

Appleshy:

Applepie: (Prompt: A Reunion)

Rarishy:

Raripie: (Prompt: A Date)

Pinkieshy:

Variety is the Spice of Life Challenge Extra Spicy Edition

Because I'm crazy, I'm playing on hard-mode twice.  The Extra Spicy Edition is the challenge again, only for these the stories are erotica.  Fifteen prompts, fifteen pairings, fifteen stories filled with ponisex.

Twidash:

Appledash:

Raridash:

Flutterdash:

Pinkidash:

Twijack:

Raritwi:

Twishy:

Twipie:

Rarijack:

Appleshy:

Applepie:

Rarishy:

Raripie:

Pinkieshy: (Prompt: A Date)

There are a handful of things you will never see in any fic I write.  I would suggest other writers follow them too.

1)  I will never refer to, depict, make mention of, or allude to wing-boners.  Wing-boners are stupid and silly.  A pegasus' wing might be an erogenous zone and a pegasus might flair his or her wings in surprise, interest, or shock, but flaired wings = erections is juvenile.  (note: I failed you, internet; this promise has been broken)

2)  I will never use the word 'plot' to refer to a pony's posterior.  The origin of this convention is amusing and it's a funny inside joke, but 'plot' is not a synonym for 'ass.'  The canon terms are flank and rump and other actual synonyms may make appearances.  Plot will not.

3)  I will never, through prose or dialogue, refer to a mane six pony as being their element of harmony, nor will I suggest, through prose or dialogue, that a character's actions are dictated by their element.  The elements of harmony chose their pony based on compatibility, and the mane six all have personalities and talents that reflect the element they are connected with.  However, they are not in and of themselves the actual element, and they are not blindly mind-controlled by their element.  This is the very reason the plot of The Return of Harmony worked; through manipulation the main cast was coerced to go against their own nature, severing their connection to the elements.  They all have an innate connection to the elements that chose them, but they are still human (err...ponies), they make mistakes, and they have to struggle against their own faults to better themselves and be all they can be.  If they're just hogtied to their element, there's no room for growth, for change, for choice.

4)  I will never reference pony memes.  Celestia will never ask if anypony likes mmmmbananas, Lyra will not want hands, Fluttershy will not cry at a tv, and Pinkie Pie will not invite Rainbow Dash over to make cupcakes.  This fandom is amazing and full of wonderful fan-generated content, but fanon that relies on other fanon is too recursive for me.  A reader shouldn't have to know about the ins and outs of the fandom to appreciate a story about characters on a tv show.  Inclusivity people, it's what we're all about.

5)  I will never use the word 'buck' as a stand-in for fuck.  I will use it when I'm on message boards or chats that have language rules and it's an acceptable way to not say fuck, but I think it's really out of place coming out of the character's mouths.  If I need the characters to curse, I'll just have them fucking curse.  It sounds kinda funny either way; the canon for these characters doesn't make any of them potty-mouths, but it's more honest and less jarring to use the real words.  Plus, if 'buck' means 'fuck,' there are a whole lot of unintended double-entendres that don't make sense.  "Yeah, Rainbow!  Fuck those clouds!"  "Man, Applejack sure likes to fuck those trees..."

6)  I will never depict a character transforming into an alicorn and I will be hard-pressed to write an OC that's an alicorn.  I get the allure and it has been handled well in some fics, but I will never do it.  It screams wish-fulfillment, and has the nasty habit of transforming whichever character (up to and including all of the mane six) into a Mary Sue.  There are three canon alicorns.  That's enough, frankly.  I won't say I'll never write an OC alicorn because I see the potential application of such a character, but I will never have a unicorn character grow some wings, magic some wings on, a pegasus grow a horn, or an earth pony get both.  That goes for the dreaded 'pegacorns,' too. (note: I failed you, internet; this promise has been broken)

Now, for things you probably will see in my stories, refer to this handy-dandy flowchart that gives an eerily accurate view into my planning process:

(Source)