My most favorite fanfic changes a lot but the current one is Fallout Equestria: Project Horizons, It's a good read and I'm pretty sure it's the longest completed fanfic on FIMfiction (around 1,750,000 words). You should read this if you've read the original Fallout Equestria.
The story series Ponies After People are also pretty good and so is the Split Second series.
One of my favorite dark fics is the story The Monster we Made.
The Hard Reset Trilogy is an interesting read, has stuff to do with time loops.
Romance is also quite fun sometimes, the fanfic that is the most in this genre for me is the An Affliction of The Heart Series.