My favourite fanfic ever would probably be either
Witches and Woodlands or
Redaction Of The Golden Witch (link to Part 1). Both are fanfics of Umineko, but are otherwise pretty different. Both require a pretty solid grounding in Umineko to understand (W&W up to EP7, while Redaction spoils all 8 EPS). If I had to pick one, W&W would win purely because it isn't 35 hours long and can actually be semi-easily reread rather than taking a whole week of free time to reread.
Both are also raised above other fanfics through good sprite work and managing to integrate the utterly amazing Umineko score, which is something most fanfics can't do.
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W&W is a (mostly) comedic story of what if George, Jessica, Maria, Battler, Dlanor, Erika and Beatrice sat down to play a game of what passes for Dungeons and Dragons in their world. George is a Monk, Jessica a Thief, Battler a Fighter, Maria a
Sorcerer Witch, Dlanor a rulebound Cleric, Erika a metagaming Paladin and Beato is the GM. Together, they must enter the magic fortress Kuwadorian, overcome the trials of the Seven Stakes and capture Beatrice for King Kinzo.
Despite the seemingly-cracky premise, it treats the whole matter with incredible sincerity and, fitting for a fanfic of a work that explored the mystery genre in great detail, discusses the role of the DM, how important story and character/player involvement is and puzzles. On specifics, The Gold Puzzle is a work of art, and the climactic final battle is worthy of comparison to Umineko's EP5 Cathedral Duel which is a high compliment from me. No-one is out of character, there are many seriously funny moments and some incredibly dramatic and intense scenes and while the ending is inevitably tragic, with the various people pledging to get together next year and continue (which is never going to happen), for the duration of the story the cast gets to have fun without crazy murders, parents tearing each other apart over inheritance or evil grandfathers.
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Redaction, OTOH, is very much a more serious work. W&W, despite it's intense moments of drama, is at it's heart a comedy. Redaction isn't. And it's also really long, at around 35 hours. So it's an investment.
Redaction is also only tangentially related to the Ushiromiya family or the 1986 massacre, and is instead focused on the Witch Hunters of 1996. It goes into just what kind of people would look at what should have been a massive tragedy and start playing with it like a logic puzzle, or to try and argue that the family was actually killed by magic, or try and "solve" it by arguing over which family members likely murdered the others in cold blood all with no real evidence or purpose besides a morbid glee and curiosity. They throw out dumb theories, spend large amounts of money on going to Japan purely to "investigate" and interrogate those who saw the family last (the boatman esp) and in general act terribly.
And then a group of them go to the island one day and end up murdered, and a new "forgery" Umineko Episode is found which seems less about the Ushiromiays and far more about Witch Hunters and guilt. And now it becomes a question of whether this forgery is a joke in bad taste, a confession or something else?
For a comparison to W&W, one of the most "comedic" bit of Redaction is a bit where Sorcerer Battler is taken to a Witch Hunter convention and is complimented on his "cosplay", but criticised for getting details wrong. Of course the comedy is swiftly murdered when Battler begins reflecting just how creepy and disrespectful the whole event is from his PoV, given how these are people playing dress up with what amounts to his family's corpses a decade after their deaths.