The Newest Challenger. After his final battle with Sasuke, at the end of Part One, Naruto is transported to the Street Fighter universe. His wise cracks, and showman bravado make the story a blast to read through, while also have a good dramatic air during the more dark and emotional bits. Naruto's desire to return home is slowly being, but not completely, forgotten and it shows how much Naruto has changed, as well how much he's stayed the same.
Son Of Apophis. Quite possible better than most published stories—with the exception of the very first chapter. Not very well known at all.
A Twisted Tale. A pretty decent Harry Potter-Twilight crossover. There was a small period of about three chapters where the author got skimpy, but got longer. Really needs more love.
The Sacrifices Arc an alternate universe of Harry Potter which presents different rules of magic, a powerful Harry, focus on minor characters of the series and try to show the point of view of anyone. Present on the internet but not detailled often.
Polarity: A different take on Spider-Man B-villain the Shocker, aka Herman Schultz, and his attempts to survive during a zombie apocalypse. Overshadowed by The Shocker Legit, this story (and its sequel "Transistor") is well-written, focuses on the bad guys in the Marvel Universe, and does it all without handing anyone the Idiot Ball.
White Rain is one of the better Narutopost-series stories out there. It starts on the opposite end of their world, a woman and her children making the journey to Konoha... and things happen.
Pipeline is a cool FusionFall fic, because it takes the Darker and Edgier aspect of the game and analyzes the results of throwing kids into a war. The resulting fic is a very good analysis told through Kevin's eyes, which is why it isn't very well known in the fandom. Dexter and Ben are the big time favorites, and while they are directly involved with the plot, Ben's only in it here and there and Dexter only has one scene. Kevin's not a very popular character because he's often been portrayed negatively (at least next to Dexter and Ben.) The fic doesn't try to glorify him or defend him, but show that his faults are what they are and that he's a good person fighting on the good side any way— even if he likes things his way.
Plasmas Folly: Despite its somewhat cliché premise, this very much ignored Pokémon fanfiction is well-written and becomes increasingly intricate as the plot progresses. It starts off slow, but it has a lot going for it.
The Pony POV Series: This Series is incredible! I mean, Seriously. Have you looked at it? 102 chapters and counting, countless guest artist signing up to help with chapters and artwork, expanding on the series, while adding tons of concepts such as the nature of Celestia and Luna's family, where Discord came from, setting all the other G's in the past of the fic, strong character development, great jokes. Heck, THEY EVEN GOT AN AUDIO ADAPTATION OF THE FIC! Why isn't this more popular than it currently is?
Chain123's fanfic The Wolf Within is a great Sonic the Hedgehog fanfic that is unacceptably underrated for its quality. It's about Tails, the last survivor amongs the Freedom Fighters after Robotnik's latest attack, trying to change the future by traveling to the past in order to stop Robotnik before he kills all the Freedom Fighters. On his trip back to the past, he becomes a member of Lupe's wolf pack and from there the story goes on. This fanfic defently deserves more than it got; that it only has 60 reviews is just unacceptable as it deserves atleast 150 reviews. You can find more on why it's good on the fanfiction reviews on the "Fanfic Recs" section of Sonic the Hedgehog page but give it a try and read it.
The Beetlejuice fanfic Life Won't Wait. It's brilliantly written and fits incredibly well with the cartoon universe. But since so many fans ship Beetlejuice and Lydia romantically, the story is ignored for strictly keeping their relationship that of a close friendship.