Harry Potter and the Methods of Rationality is one of the best books that I've ever read, and yes, it is a book more than it is fanfiction. As multiple reviewers have noted, more thought seems to have gone into this than into the actual HP books, and into ensuring that there are no dastardly, for-the-lulz evil villains, magic based handwaves or storms of cliches. The HP:MOR world works in a way the original doesn't, simply because it makes a world of magic so believable that it's hard to realise that someone actually sat and worked out rational explanations out after Rowling had already had a bash at it. It is a must read for anyone even vaguely interested in the Harry Potter universe, as long as they don't mind the occasional author tract.
On that note, Lightning on the Wave's Sacrifices Arc, which starts with Saving Connor. A fascinating AU, and one that truly deserves to be called an AU: the characters have been stripped down to their basic selves and set in an entirely different situation, but react to it the way they would were it canon. With the except of Lily, perhaps, everyone fits their characterization like a glove, and there are no handwaves. This is a fic that manages to make Harry a Slytherin and friends with Draco, among other things that I won't say in case someone wants to read it, and it works, beautifully and tightly. Lightning introduces his/her OC's so well that multiple people have said they thought they were canon characters that simply didn't get enough time in the original books to make an impression, and this troper for one has been surprised at the mention of characters in other, unrelated fics that I'd thought were OC's. It is the only fanfic that I will say this for: were it not for its dependance on Rowling's world and characters, it would be published as-is, with the exception of about three typos per book (there are seven "books", getting longer as the story progressed beyond what Lightning had originally intended). Granted, it would be shelved strictly in the adult section, but I find myself not wanting to go back to a universe that doesn't contain these characters and situations.
Sam Vimes/copperbadge is absolutely brilliant. His Stealing Harry/Laocoon's Children AU series is what Harry Potter would be in a better world, and all of his other series and stories are so wonderful I want to hug the screen. I could go on and on about how wonderful his fics are, but I will say this: that man truly does Remus Lupin justice.
I love Yuletide Treasure. If that archive were a person, I would marry them. During the time it was down for Christmas I was so sad at being cut off from the fun experience of finding stuff for fandoms you never knew you had that... I started writing again. I hope to contribute to it as soon as I can myself. And just for an extremely random taste of things— this gushing comment was brought on by rereading Small Monsters again. It was the last awesome straw that broke the awesome camel's forcefield protecting it from becoming more awesome. And now it's even awesomer.
Titan Legends. A fanfic that could probably pass for a highly obscure alternate DC continuity in and of itself.
Tony's Mansion of Heroes is one of my favs. It's not perfect but it brings together several characters from different universes to save the Worlds from familiar to obscure villains. You get Sora, Riku, Glitch, Stitch, Peter, Kaiba, and several others to stop the villains' plan to resurrect the Dark Gundam and the dragon creature known as Kikros. It seems that the writer has recently began to fix his earliest chapters. Spacing out paragraphs better, getting rid of subplots that haven't gone anywhere since 2005, and it's looking better.
Eyrie Productions' works, especially Neon Exodus Evangelion. This fic is great, I love the plot twists, long digressions, painstaking research, and Alternative Character Interpretations. I even love DJ Croft no matter what anyone else says. And the ending is simply one Moment of Awesome after another.
I can't speak for NXE, but the EPU's flagship work, Undocumented Features, is frankly a little frightening in terms of sheer scale (hundreds of megabytes of plaintext!) and awesomeness. Even the "crap years" are very entertaining (thanks in part to excellent use of Rule of Cool), and it quickly gets awe-inspiring.
This troper is writing a serious literary analysis of Full Life Consequences.
4Paws Studios' "Buffy The Vampire Slayer: The Chosen" is, to me, the definition of what a good Fix Fic should read like. I was referred to it by this very Wiki, and haven't looked back. There isn't a page for it yet in the Fanfic section (why?!), but it's miles and miles of good characterization and character development, humor, tenderness, and a generous dollop of awesome. It's like the Buffy-fic equivalent of rich, fulfilling chocolate. ^_^
It breaks this troper's stupid little heart that he seems to be the only one to have read X to the Zoltan's Godzilla Daioh crossover series. Sure, it sounds crazy, but it's better than it sounds! Or even better, his Azumanga Daioh / Star Wars fusion! The writing, the characterization, the tragedy, it's SO GREAT! AAGHH, why does this reduce me, normally The Stoic to a little pile of heart-wrenching joy and love and sadness every time?! It is this troper's dream that this author return to (Azu Dai) fanfiction someday...
whydoyouneedtoknow's Harry Potter AU Dangerverse and associated AUs (yes, AUs of AUs) have been called "better than canon".
This trooper really likes The Great Disney Adventure and it's growing sequel on Fanfiction.net. Though technically unoriginal since it's interpretations of the movies have the same ending, it has several saving factors. 1. It throws some original characters into the mix/ characters that don't belong in the story. 2. It takes the effects of it's main character more seriously than one might expect. 3. It's super funny. 4. It has a lead female who's not only cynical, but also pushy, realistic, and sly; hardly Disney hero material, and watching her interact with our childhood's favorite characters really makes it for me. Plus, it's got Pirates of the Caribbean messing up all the movies ever so slightly.
Manchester Lost and its marvelous sequel, Paradise Thwarted. Wonderfully hilarious fanfic that lampshades itself to the moon and back, yet it still has time to go through a marvelous plot and sweet moments of complete fluff.
Now, let's not be so hasty as to simply post the fic. Let's explain why this thing is a total masterpiece. It's a cocktail of insanity, a twisting of plot so horrendously bizarre that it stops being stupid and becomes what could possibly be called PureSpiralEnergy, engulfing the reader in its amazing attitude, incredible nature, and disregard for rationality all in one amazing package.
Code: Total Drama Reality is an excellent blend of the Total Drama and Code Lyoko series, which sounds a bit far-fetched at first, but Lord Maximus is able to squeeze every bit of adrenaline out of such a premise and make a completely awesome crossover. It's also recommendable by how LM keeps characters from both shows intact, even coming up with rather Tear Jerker backstories for quite a few as well as the chance for several Total Drama favorites and Aelita to take major levels in badass.
My Immortal could easily be the best ever example of So Bad, It's Good. This is the most genius troll fiction (it must be!) I have ever read, and it probably made me laugh more than anything else on the internet.
Light and Dark The Adventures of Dark Yagami is a brilliant, hilarious Troll Fic. But what sets it apart from the crowd is its unique execution; it doesn't just rely on poor grammar and Rouge Angles of Satin. No, it contains not only all the good qualities of your standard troll badfic, but also a wonderful sense of humor that will leave the reader in stitches. An amazing read that will have you laughing for days.
I, Grognor, love the Hell out of Harry Potter and the Methods of Rationality. I never read Harry Potter, I don't understand four-fifths of the references, and I'm missing probably all of the subtle foreshadowing. I still love it. When I first started reading it, I couldn't do anything else for several days.
The Interloper is a realistic take of the future after the ending of Digimon Adventure 02, it starts out giving you the fact that humanity simply hates digimons rather than loving them, and that there had been a war between Humans and Digimons for three years, currently, it's a fanfiction in work... But the author, The Silent Insomniac on fanfiction.net proves to spare no expense when it comes to the story, all of his chapters take on absurd detail about everything, everything, there is also an OC called Christopher Van Numen who, while he is a Sue Power-Wise, proves to be a very, very interesting character, the author even goes into absurd detail on his backstory and Christopher isn't even one of the Main Characters. Absurd word count - over 400k words up to chapter 23 - but definitely worth a read if you care about Digimon at all. Forewarning: Battle chapters tend to be gory
No meantion of Fallout: Equestria? It is a story that I still adore after finishing it months ago. It has interesting characters that are believable and easy to care about. The two different universes seem to mix perfectly, and the atmosphere is pulled off flawlessly. It is an emotional rollercoaster that will leave you shell-shocked.
Poké Wars is an absolutely amazing fan fic. Realistic character interactions, well developed characters, great worldbuilding and a great plot all combine to make this a hell of a story. Add absolutely dazzling fight/action scenes to this and you have a winner.
Homeless Two Tail is the greatest Sonic Fanfiction featuring tails as the main protagonist. It's moments funny, heartwarming, sad, nightmare fuel, and awesome are stupendous. It's Character's are pretty cool, too. All of the characters from the official media are portrayed nearly identical of what they're like in the sourse material. Although there are a few exceptions, this is not a bad thing. It's also one of those few fanfictions that uses fan characters that aren't Mary sues. Smoke stack is a really cool character, Igneous Rock is flippin' hilarious, Karst Ice is an irredeemably evil villain with quite the ego, and Hang Nail is a character who is a monster of the highest caliber , especially when he comes back.This. Fanfic. Needs. It's. Own. Page. With it's own Character Sheet, Crowning moments of funny, heartwarming, awesome, tearjerker, and nightmare fuel pages.
A Second Chance At Life (Miranda Flairgold), anyone? The single best AU Harry Potter fanfic I have ever found. Reasonable divergence from cannon, brilliant O Cs, and even some elements of the original thrown in for flavor. Also: time travel! Dragons! Vampires! Animagus forms! Space elves! And more! Currently in the third story out of an unknown number. Hasn't been updated in a while, but Flairgod is still active on F Fnet, as far as this troper can tell.
[[Tropers/Timeskipper This troper]]'s favourite fanfiction so far could actually be Scar Tissue, a Neon Genesis Evangelion post-Third Impact fanfic. It's very, very dark, with a premise (After the events of End of Evangelion, while the world is trying to recover from the catastrophe, Asuka, now living with Shinji, has been brutalizing him in every possible way, while he accepts everything she does to him because he thinks he deserves it for what he's done in [EoE]. The story starts after Asuka, in a fit of rage, has beaten Shinji so hard that he ended up in hospital, and she realized how much she was hurting him, and tries to make amends) that may make some people cringe, but it actually handles very well the characters' psychology, reaches repeatedly the peaks of heartwarming and depressing and, while it is fairly dark, the way it deals with the characters' efforts to heal the scars left by the events of the series and eight months of an abusive relationship that wounded them both even more deeply is very, very touching and it leaves a wonderful message of hope. It's very sad that the fic hasn't been updated for an year, especially now that we had learned that SEELE hasn't disappeared and has decided to take its revenge against NERV. It's still a read that I would suggest to anyone who knows what Evangelion is. And even those who, as I did the first time I read it, don't know it.
Best Laid Plans by dfastback68. I mean, dfastback68 takes two tiny characters in Revenge Of The Fallen and gives them an amazing backstory that makes me want to gush forever. It's sets up the background wonderfully and really fleshes out Demolishor's and Sideway's characters, complete with all their little quirks (westerns vs. horror...ha). AND it has cameos from Barricade, Scorponok, Soundwave, and the Constructicons. With no grammar or spelling errors. And it does not get the attention it deserves - it's heartwarming, in-character (to toy bios), and the ending... gah, it made me CRY. Not in the happy way, either. To sum, Best Laid Plans is fucking awesome, and I have not found a better fan fiction yet.
The North Remembers by SilverRavenStar doesn't just set the standard for ASOIAF fanfiction, but for fanfiction in general. The author's intertwining of all the intertwining plotlines integral to the series and characterization is so spot on that you'd swear George R. R. Martin himself was writing this.
The New Look Series by Shinnok has some of the best stories about crossdressing fictional characters I've seen in a while. Most of the stories have well-conceived characterizations and a healthy amount of Mythology Gags in the universes the stories are based on. Everyone is in character, it's funny, well written, and overall very good fanfiction (with the exception of Naruto's New Look which even the author didn't like).