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These are my all-time favorite (completed) ponyfics, and a subset of "Recommended", though this list probably says more about me than about the fics.
I wholeheartedly recommend these (completed) fics to anyone who finds the tags and premises appealing. These are not merely good, but exceptional.
Every complete or incomplete fic I have read from start to finish, regardless of my opinion on it.
Incomplete fics I've read up to the latest chapter, have been updated within the last 6 months, and will probably get added to "Recommended" when completed.
Read It Later fics that are either >200k words, or the start of a series/AU/etc that adds up to >200k words
For every million-word epic, there are countless tiny ficlets that are best organized by author. Currently, this is a list for: ambion
Incomplete fics that I’ll want to try reading if they’re ever completed, but probably not until then.