I'm a late comer to American comics, but I grew up on the European Tintin and Asterix. Those universes don't attract much fanfic, maybe because they lack the two big adult themes: sex and death. This story, in essence, introduces the latter to a world where it previously didn't exist ... not through death itself, but through the simple passage of time and the necessity of making changes. Melancholy, yet ultimately hopeful.
I've never opened an issue of this comic, but I didn't need to in order to appreciate this story - the characters and their situation are painted vividly enough. It's all about love, and leaving marks, and belonging to people.
Another comic I haven't read, but I have heard the author talk about it and read enough fanfic to know that the journey the protagonist takes is down a road that many have walked before him. This is the story of one such person - a universal story with an individual spin and an engaging original protagonist.
Say what you will about Warren Ellis, he has the best Mary Sues. I love reading about the adventures of Spider Jerusalem - he's an enormously fun character to base a comic around. Up close and personal, though ...? Maybe not quite so fun. Here he is, years after his death, from the perspective of one of the Filthy Assistants. Both characters captured with rare perfection and a refreshing lack of sentimentality.
I've never encountered the Badger outside of this and the one other fanfic I've ever seen starring him ... and I actually think that may make this story even better. If you don't know what's going on, the twists and the sad ending are more surprising than they might otherwise be. Fine fanfic about a character people have hardly heard of, let alone written about
Why, look, it's Watchmen fanfic! Fanfic worthy of the Watchmen name, what's more. This picks up where Alan Moore's brilliant series left off. Ozymandius is still with us, and Rorschach is ... not quite as dead as one might reasonably expect. Dark Mark has a well-deserved reputation for writing about obscure characters, and it was hard to pick just one story for this list, but I couldn't go past this.
Lazarus Churchyard is an early work by Warren Ellis, set in a dark, dystopian future full of seriously messed-up people with really fucked-up stories. Anyone who's read it will know that the tale of Lucy may be the nastiest of them all. Surely there couldn't be a way to make it worse? Amanda Sichter managed to find one.