Life and Times of a Winning Pony and Earth & Sky are both sequels, but their respective root fics are short, enjoyable reads and the fics themselves are definitely on my "drop whatever I'm doing to read them list" when they update. Background Pony you probably already know, since everyone seems to have it in their top favorites and it's catapulted SS&E to instantly making the feature box with all of his uploads (or is SS&E a her?). Keeping It Simple is my favorite depiction of Mac ever and it's a great mix of warm fuzzies and sad moments. Treasure in the West takes a concept that sounds like it couldn't possibly work played straight, then plays it straight gloriously. Read it.
[Comedy] [Slice of Life] Spike is no longer the chubby baby dragon he was, and he no longer has to go through his hundred-year wyrm sleep. But as he and Twilight move back to Canterlot, Spike finds that his new larger body means the end of his old life. 30211
[Romance] [Slice of Life] Rainbow Dash teaches a preteen Scootaloo how to fly, strengthening their bonds, both to each other and the ponies around them. A story about love, family, and growing up. 72115
So, my favs list has expanded, and I can't fit all my recommendations in one spot anymore!
First up, we have "Finding Your Place," the sequel to "Under a Luminous Sky." It's a very different beast from its predecessor, focusing on Spike, who has suddenly found himself the equivalent of a hundred or two years older in the space of moments. Ponies are terrified of him, he can't fit inside anywhere, and he'll have to watch all his friends slowly die. Oh, and it's tagged as comedy.
"Spellbound Fireflies" is about Scootaloo, getting lessons from RD (about flying) and Twilight (which is general tutoring), who RD is dating. It's sweet, very poignant, and unlike too many fics, actually portrays a romance that's ongoing and positive instead of watching the relationship start/end. Also, bats is the god-emperor of TwiDash and you should probably read the rest of his stuff.
"Book of Days," by returning-to-my-recommendations author Warren Hutch is told as a diary from Clover the Clever (annotated by Twilight Sparkle) detailing the origins of Celestia. And maybe Luna down the line, it remains to be seen at time of writing. Clover quickly becomes Celestia's caretaker. This one I really recommend because before this I'd yet to see an origin for Celestia that was particularly satisfying. "Book of Days" fixed that with an origin that makes so much sense that it reads like canon. Also, filly Celestia is adorable.
"Only Human: A Lyra Heartstrings Production" is definitely among the more interesting ideas I've seen, if nothing else. It follows Lyra as she gets a show greenlit about her favorite creatures she made up - no points for guessing what creatures those are - and then the entire creation process in a story that I'm guessing mirrors the creation of MLP:FIM. (Having not looked up the specifics, this is just an assumption, but what I do know just from this or that factoid that pops up in the fandom's general chatter, it seems like a good guess.)
And then we have "The Lunar Rebellion," by also-returning-to-my-recommendations author Chengar Qordath. It takes place in the exact same continuity as the rest of the Winningverse. It is nothing remotely like the rest of it. The main character is Shadow Kicker, who is Cloud's ancestor of roughly 700 years before the main canon. She's an ephor within the government of Pegasopolis, which at this point in time is an autonomous state like the other two tribes, just allies under the joint rule of Princess/Commander/Chancellor Celestia. It's about Shadow's political dealings, and the growing unrest within Pegasopolis at having a distant leader who as they see it can't be bothered to actually do anything herself. Personal favorite character in this one has to be Archmagus Sunbeam Sparkle, though, who is Shadow's foremost political rival and Vizier to the Princess. She's just a deliciously awful pony.
And holy crapnuggets, did I ramble on this one.