Dont forget these

Night of the Werepony Fluttershy goes under a few personality changes after being bitten by a werewolf. by Azure-Spark 14,362 words · 601 · 11
White Box Here in the White Box, the lights hurt my eyes. by chrumsum 11,392 words · 1,951 · 38
Better Living Through Science and Ponies Not all is well in Equestria when a failing portal gun brings Aperture Science to the land of ponies by Pen Stroke 39,979 words · 3,433 · 65
Cold Lightning Something about Lightning Dust just seemed a little 'off'. by nodamnbrakes 7,105 words · 404 · 45
Overpinking It Ponky likes Pinkie Pie, and she likes him. Maybe? It's hard to tell. by PropMaster 25,037 words · 256 · 11

These too

Sunny Skies All Day Long Celestia's Day Off by PhantomFox 8,536 words · 9,449 · 145
My Little Dashie What would you do if you found a Filly Rainbow Dash in a box? by ROBCakeran53 12,524 words · 13,346 · 819
Gutterloo In the cold winter of Ponyville a single spirit walks alone. by jmj 6,822 words · 233 · 22
Twilight's Life We all know of Twilight Sparkle, the hero of Equestria.But what was before that? by DuskShadowTheArkane 66,439 words · 1,299 · 23
Mort Takes a Holiday The Pale Pony (of Death) faces his greatest challenge yet: free time. by AnonymousMaterials 166,617 words · 4,401 · 79

The Things We Leave Behind A year after a tragic incident, Twilight Sparkle returns to Ponyville to visit her friends. by theswimminbrony 23,097 words · 1,407 · 34
A Simpler Time Two friends realize their friendship goes back farther than either of them ever realized. by DJLowrider 4,130 words · 3,115 · 41
Ponyville Pawn Stars You never know what's going to trot through the door of the Silver Saddle Pawn Shop... by TimidWolf 66,771 words · 151 · 4
Would Anypony Miss Me? Some things are just to much for certain ponies to handle. by Regidar 32,057 words · 94 · 16
A Sun Without A Moon After Celestia humiliates her at a dinner, Luna storms off and ends up snooping around in her sister's room. There, she stumbles upon the journal Celestia kept immediately after the banishment of Nightmare Moon. by Mourning Zephyr 4,682 words · 2,113 · 26