Favourites (random order)

Blue like Sapphires Its the aftermath of the Ursa Minor, what will Trixie do? by ambion 11,602 words · 96 · 3
Diamond Tiara Makes a New Friend Takes place immediately after Bad Seed. Diamond Tiara is feeling down, when a new, unpredictable friendship is offered to her. by Yukito 2,968 words · 80 · 0
The Flight of the Alicorn Rarity finds herself forced into an unlikely alliance when her airship crashes far from home. by Ponydora Prancypants 227,108 words · 1,444 · 28
Harmonics Years after the events of Discordant, Scootaloo is hired as an assistant flight instructor. by ezra09 183,990 words · 618 · 19

Not all of these are stories I consider "the best" but they were some of the ones I enjoyed the most.

Continued

Millennium Wake: Part 1 What happens after a certain pony awakes from a magical slumber after a thousand years? by Chaotic Dreams 112,664 words · 991 · 34
The Proper Care and Feeding of Monsters Fluttershy discovers the limits of compassion. by Cold in Gardez 6,561 words · 632 · 7