Favorite Worldbuilding Stories

The Moon's Apprentice Twilight Sparkle failed her entrance exams for Celestia’s school. Worse, she is a danger to both herself and others, resulting in her magic being suppressed. Dreams crushed and now one of the weakest unicorns, a nightmare comes to her. by Forthwith 412,134 words · 3,803 · 174
Daylight Burning The return of an ancient enemy draws the ponies into a deadly spy game. by Guesswork 71,200 words · 740 · 33
A Dream of Dawn What if Luna won against Twilight? What happens when Discord comes back? by Starsong 137,251 words · 1,781 · 32
Sunset of Time Sunset Shimmer: Princess Twilight Sparkle's most faithful student. After bearing witness to the End of the World, she travels back in time to destroy the Dark Regalia and save her future. But a ghost from the past has other plans... by Albi 232,768 words · 1,357 · 36

Stories which do an excellent job not only portraying the world of Equestria, but in expanding and building upon what is there, adding new explanations for questions previously unanswered and providing creative and thorough backstory for the history of Equestria. In the field of worldbuilding, these are the master architects.