Writing one myself, so it is only natural that I enjoy fanfiction works. There is a couple of them that I would recommend.
Fanfiction Downloader Not a actual fanfiction, but it is a useful tool if you want to download a copy of a story and to convert it into .pdf format. This is quite handy for me, so I thought to mention it.
Megaman: Guiding Rainbow's Light This one acts as a precursor to the Megaman series, explaining how various technologies in the games like treeborgs have come into existence. As such, the focus isn't on robot characters, but on Dr. Light and Dr. Wily before things went wrong. It should be noted that this fanfiction could be considered a part of the Legacy of Metal series, in which various authors cover one or more Megaman games and then connect their lore together. I consider Guiding Rainbow's Light to be very good at presenting the human characters, and really enjoyed the world building.
X-COM: Enemy Unknown (PDF) While not as good when compared to Guiding Rainbow's Light, it is a pretty nice and lengthy take on the original X-COM. It captures the feel of the game quite nicely, but also has elements of the X-Files and other conspiracy theory material.
Fallout: Equestria What do you get when you put techni-colour ponies, megaspells, and the future in a blender? Fallout of the Equine kind. I think this fanfiction is one of the best representatives when it comes to merging two fandoms together, as the story is able to capture how Equestria fell from what we knew in the show into a desolate wasteland. This actually evokes the atmosphere of the Fallout series just right, that I can safely say that it can stand next to Fallout 2 and New Vegas with pride.
Ellora the Archer This is probably one of the earlier Let's Plays that have been done, so I consider it an archaelogical piece of sorts. This one follows Ellora, an archer who has entered the Mazes of Menace. I couldn't find any places to download the .pdf, so I uploaded it for your reading pleasure.