My personal favorites

Love Can't Be Programmed Twilight magically transports herself into her computer, and she finds a sexy surprise. by SwiperTheFox 7,154 words · 202 · 10
Griffin the Griffin Name's Griffin, I'm sarcastic, I'm crude, and I'm a brony. by BlackWing 345,583 words · 3,424 · 294
The Doctor Dances Doctor Whooves is trying to find his way back to our reality, but perhaps he could stay... by Gallifrey 6,942 words · 792 · 18
In Which A Pony Gets Diabetes ...and it's not the end of the world. by FredMSloniker 1,173 words · 63 · 3
Through The Eyes Of Another Pony Stupid Human takes a trip to Equestria. But not the Equestria that he was wanting. by CardsLafter 167,923 words · 2,914 · 211

Other Storys i like

My Little Caboose: Blue is Magic! What happens when the Reds and Blues finally get Church out of the Epsilon unit? Caboose decides he wants a turn in the unit, of course! What happens next? Well let's just say he always did say he wanted a pony, now he has a world full of them. by DarkWing 343,908 words · 2,853 · 139
Hands A slightly more realistic take on the "Human in Equestria" story concept... For a given value of "realistic." by Andrew Joshua Talon 163,998 words · 4,662 · 339
Pipsqueak's Day Off It's Friday and the teenagers of Ponyville have a day off school. Shenanigans and shippings ensue! by Neon Czolgosz 47,721 words · 626 · 27
Journey to My Imagination In a strange event, Lauren Faust is teleported to Equestria. by DeiStar 94,438 words · 2,602 · 136

You should read these they are really good

Researcher Twilight Twilight delves into research considered taboo and off-limits by the Equstrian Diarchy. by NATOstrike 93,373 words · 1,207 · 53
Borderline Dwelve into the mind of the famous Cupcakes killer, Pinkamena Diane Pie by Lucefudu 13,484 words · 642 · 33
The Most Important Pony In Your Life Scootaloo ties to take her own life and Rainbow tries to help her. by ColeTrain4EVER 11,223 words · 287 · 12
Shut The Blinds Rainbow Dash is blind. by The Rainbow Blunderbolt 75,542 words · 2,143 · 101