Top 5

Eternal Princess Celestia and Twilight Sparkle's bond is tested by miscommunication and guilt. by device heretic 159,827 words · 3,072 · 66
The Night is Passing Celestia disappears, Equestria falls apart, and Twilight goes West to recover her lost teacher. by Cynewulf 525,472 words · 941 · 63
Hard Reset Twilight gives her life to stop a changeling invasion. Repeatedly. by Eakin 36,358 words · 8,208 · 134

These are fantastic. Must reads.

Favorite Comedies

Clop It! Twilight Sparkle and her friends awaken to find themselves in Straight Camp. by PrettyMonster 65,837 words · 1,399 · 148
Ethanol, Elements, and Estrogen What happens when you Seth Rogen the Mane Six, give them alcohol, weed, make them randy, and love struck? Have Rainbow wanting a lover, Twilight to lose her virginity, Rarity plan the personal lives of everyone, and nearly no moral compass? This. by KiltedKey 142,732 words · 646 · 76
Six Brides for Two Sisters After spending Nightmare Night in Ponyville, Luna decides on how to reward the six mares who defeated Nightmare Moon and saved her from herself: Marriage. by Equus Pallidus 52,728 words · 2,381 · 69
Rainbow Dash Dies An Awesome Death Rainbow Dash is telling her friends in the library about the story of her death and how it was worth it. by Diablomuerte2 2,451 words · 179 · 29
Spring is Dumb Rainbow Dash definitely didn't do anything wrong. Rarity is the one who's wrong. Rainbow Dash is absolutely, totally, a hundred percent sure of it. But then why did she just buy a wagon load of apology bouquets? by HoofBitingActionOverload 9,255 words · 1,406 · 39

These are all great comedies. "Clop it!" has some of the best lines i've ever read. EE&E is absolutely raunchy and over the top. 6B42S first two chapters are spot on for how the characters would react. Spring is Dumb has one of my favorite Rainbow Dash portrayals.

Best Romances and Shipping

A Year of Seasons A glimpse into the love and life of Rainbow Dash and Fluttershy, as told over the course of a year - a year of four different seasons that span a lifetime. by The Rising Tide of Night 30,044 words · 141 · 9
The Shadow of a Doubt Nights in Canterlot are for sharing secrets. Ten years have passed, and the six friends have begun to walk their own paths. A burdened princess meets a friendly face among the crowds. by Ardensfax 19,681 words · 436 · 8
Under the Aurora On a sleeper train in the frozen north, sleep is eluding two travelers. by Ardensfax 7,501 words · 775 · 14
The Games We Play Somepony is once again masquerading as Mare Do Well, and it's up to Rainbow Dash to figure out who. by AbsoluteAnonymous 137,602 words · 1,992 · 59