The best I've encountered

Background Pony "My name's Lyra Heartstrings, but you won't remember anything. Listen to my symphony, for it by shortskirtsandexplosions 432,377 words · 6,806 · 242
The Party Hasn't Ended Pinkie's unrequited love for Dash precipitates an adventure across time, space and dreams. by butterscotchsundae 56,037 words · 908 · 30
Libera Mé Set just after the events of season 3, Twilight Sparkle and her friends must rise to a challenging beast the likes of which will test her not only as an alicorn, but as the Princess of Friendship. by EZTP 189,956 words · 115 · 4
A minor variation No sonic rainboom. The Mane 6 find different destinies. See where it takes them. by notMurphy 144,556 words · 932 · 39

Worth a look

Faster Rainbow Dash is given a chance to make her heart's desire real: to be the fastest pony alive. by Einhander 17,493 words · 1,070 · 33
Flitter One changeling was already inside Canterlot... and he was as surprised as the ponies were. by Nyerguds 27,410 words · 3,484 · 48
Memory Pending An outsider finds himself flung into Equestria, and forced into a new form. Will he fit in? by Kiroberos 106,466 words · 3,279 · 102
Forgiveness Pending Moon Mender's adventure continues right where left off. He jumps at the chance for a new life, but will his old one truly leave him in peace? Some things are better off forgotten. by Kiroberos 1,047,449 words · 2,253 · 118