The Infinite Loops. The idea is that something has happened to Yggdrasil, the tree-computer that contains and runs the multiverse. Universes are put in safe mode (i.e. time loops) while the damage is fixed. Each universe is maintained by an Anchor, who is the first person to notice the looping, and is always Awake (a term for being aware they are looping and remembering previous go-arounds) in any given loop. More people gradually become aware of the Loops as repairs to Yggdrasil continue, but are not always Awake in a loop. Fused Loops allow characters from different universes to interact; also, Loopers are pretty much always stir-crazy from looping. Hilarity inevitably ensues.
Horseshoes and Hand Grenades is a darker retelling of Fourze that brings in multiple Kamen Rider characters from prior series, but also uses characters from the show itself that also get involved in the madness. It also has multiple stories that expand more on Gentaro's past and his struggle in being evil and tells of how the world starts to fall apart over a single incident.
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.
My Little Megas XLR. A perfect blend of Megas XLR and My Little Pony: Friendship is Magic. It even has the omnipotent button.
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.
The New Look Series created by Shinnok Raiden 99. While some of the stories are less than great like Naruto's New Look (which even the author didn't like), the other stories are great with well-conceived characterizations, a healthy amount of mythology gags, and the stories never get real dirty like a fair chunk of crossdressing stories. But despite that the series isn't as well known compared to other fanfic series.
The Pokémon fanfic No Antidote: One of the best fanfics I have ever read. It's definitely miles above anything that has come out of the official canon story wise.
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.
Plasma's 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.
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.
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?
RainbowDoubleDash's Lunaverse, an alternate universe where Celestia turns evil instead of Luna, where Trixie is the Element of Magic instead of Twilight Sparkle…and it's much more than that. There is a lot of development and World Building of an Equestria that fears the sun. The Lunaverse is a fanfiction series targeted at an older audience than the TV show, and thus is somewhat darker, though it's not written as overwhelmingly so. The overall feel of most stories should be hopeful, yet guarded. Friendship is still at the core of solving problems, but it also requires work and patience (not that this isn't required in the show - the fact that it requires such, however, is emphasized more). Responsibility is a major theme: both keeping to your responsibilities, and taking responsibility for things you've done.
And expanding on that is The Cadanceverse, an alternate universe made by Lunaverse alum GrassAndClouds2 where Princess Cadance is the ruler of Equestria and both her aunts have turned evil. Here, the "team leader" is not a unicorn who takes the Element of Magic, an earth pony named Octavia Philharmonica who bears the Element of Honesty. In a sentence, it can be summed up as My Little Pony: The Song Fic Universe.
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.
Son Of Apophis. Quite possible better than most published stories—with the exception of the very first chapter. Not very well known at all.
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.
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 amongst 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 criminally unnoticed The Calvin, Hobbes, and Paine Show. It's a piece of metafiction about a world where Calvin and Hobbes was actually a television show, and after Watterson left it was retooled into a Variety Show and changed a lot — for the worse, Calvin thinks. The story centers on Calvin, now a jaded actor, thinking back on how the show came to be this way and wondering where Watterson went off to. The writing, while heavy on the cynicism, still retains a bit of hope, and the descriptions are wonderfully written.
The Great Disney Adventure Saga. This fic has a great leading character, fun interactions with the disney canon, Pirates Of The Carribean as a center stage, Pixar, and it doesn't follow canon unless directed to. While technically something of a self-insert fic, it's still funny, heartfelt, and sometimes even genuinely surprising. Please, enjoy, even as it continues to unfold.