One of the things I love about fan fiction is the multiplicity of it - the number of avenues you can explore, questions you can ask, middles and endings you can try. Sometimes, those middles turn bad. Sometimes, so do the endings. These stories all explore how characters change in the wake of seriously unfortunate events.
Best FF That Hints Delicately at Horrible Things, Proving That It Really Is Worse in Your Imagination:
Close Enough, by Helen. Harry Potter, Harry/Ron. This is a pairing that usually doesn't work at all for me; it just makes no sense for Harry and Ron to be romantically involved. But in this universe, Harry and Ron belong together. In this universe, no one ended up quite how they, or we, would've expected. The war changed them all too much. This story also features that rarest of beasts, a believably good Draco.
Best "What Happened After the Story Ended?" FF Ever:
Living Arrangements, by afrai. Good Omens, Crowley/Aziraphale. This one's a jaw-dropper, pure and simple, because it makes so much sense. It works so well. There's a punishment for saving the world - a punishment as cold and logical as Heaven and as vindictive and vicious as Hell.
Best FF That Explains Why It's Better to Talk:
Paying Silence, by Mairead Triste. The Sentinel, Jim/Blair. In this one, Blair can't find the words, and he pays for it over and over. Not one of the happy stories so common in this fandom.