Background Pony: Nuff said.
Harmony Theory: This has to be one of the most under rated, under appreciated fic of all time. It takes the concept of one of the mane six (dash) and putting them a thousand years misplaced in the future trope and actually makes it believable. It actually seems like a plausible future of the cannon we have been given. No human tech or humans. Not to mention it has great characters, world building(best thing about it), and no shipping.
The Sweetie Chronicles: Its Wanderer D so you know its good. Lol, in all seriousness I absolutely love the concept of making a fanfic of other fanfics. Not to mention I have found a few new fics through it and got a bit of nostalgia with some.
Don't Go Outside: Another greatly unappreciated fic. It takes the old idea of zombies and makes them new again. zombies afraid of the dark? Genious! Also this quote, "To late Shitlight Sparkle! You lose!" priceless.
Glim: Sequel to "Not My Destiny", this has to be the best twilight turn into an alicorn fic. I have to admit I was a little wary starting this after reading the cannon appendix of the first one but dang! its good.
Honorable mentions definitely go to Fallout Equestira Memories and pink eyes. Best side stories IMHO. I like how neither of them don't have that serious tone or self loathing as the original, Horizons, or Heroes. Anywho, these are my personal favs and I wish I could add so much more but this has gone on long enough. Not like anyone will ever read this or cares about my opinion lol...