Outside of those mentioned, all from 2012 or so:
University Days (one of the original vinyltavia shipfics)
Antipodes (a rather forgotten early au adventure fic that competes with modern staples)
A change of face (short and sweet, early bon bon is changeling story)
Upheaval: Breaking Point (this is a longer series with at least 2 sequels, but an amazing AU)
Austraeoh (The longest series on the fucking planet, but dear god is it good. Read this adventure AU only if you don’t mind losing your life and never being able to read another fanfic again without having to shelve this.)
Never read but IK are popular:
On a Cross and Arrow (the fic famous for popularizing the genderswaps),
Shipping and Handling (p1k made a great song about it too!),
My Roommate is a Vampire (very popular early vinyltavia shipfic and possible origin of vinyl’s red eyes)
Allegrezza (Same as above)
Heard good things, idk the premise. Still classics:
Stairway to Equestria
Project: Sunflower
Lost Cities