What are the best stories of My Little Pony on Fan Fiction?

This is a matter of opinion. Some of the best might include:

"A Voice Among the Strangers" by Tystarr

"Fallout: Equestria" by Kkat (dark)

"It's a Dangerous Business, Going Out Your Door" by Jetfire12

"It Takes a Village" by determamfidd.

"My Little Dashie" by ROBCakeran53

"Past Sins" by Pen Stroke

"Project: Sunflower" by Hoopy McGee

"Through the Well of Pirene" by Ether Echoes