I used to detest the very idea of fanfiction, but I changed my mind after reading a few truly excellent ones, mainly thanks to the TV Tropes recommendation pages.
Assassin of the Opera [http://www.fanfiction.net/s/6407330/1/Assassin_of_the_Opera]: An Assassin's Creed 2 fic. Have you watched Avatar: The Last Airbender? Remember the Ember Island Players? Yeah, it's that. And it's brilliant. For those who don't know what that is, here's another example of the same concept from Batman Beyond [http://www.youtube.com/watch?v=K2p02DfyzCE] (Embedding is disabled for some reason. I don't understand why people do that). Needless to say, Ezio isn't amused either.
A Thing For Redheads [http://www.fanfiction.net/s/3741724/1/A_Thing_for_Redheads]: The author classifies it as a TMNT/Marvel crossover, but it's really more of a TMNT/Spider-Man fic with a couple other guest stars. I love the parallels drawn between characters, and by the end of it I really felt like these two franchises could co-exist seamlessly (Which makes sense, given that the actual TMNT origin story ties into Daredevil. No, really. Click this link and scroll down to #1 [http://www.cracked.com/article_19323_6-movie-tv-universes-that-overlap-in-mind-blowing-ways_p2.html]).
The Mysterion Mythos: Cthulhu Fhtagn [http://www.fanfiction.net/s/7086175/1/]: I saved the best for last. This is a South Park fic, a continuation of the Coon & Friends trilogy, seven years after that story arc takes place. The characters are now in high school and Coon & Friends, now called 'The League' by everyone except Cartman, is no longer just a little kid's pretend game. As the title suggests, the main character here is Kenny/Mysterion, and he's been trying for years to find out more about his curse. While Kenny's the focus, the story switches perspectives between him, Stan, Kyle, and Butters, the latter of whom is now a cross-dresser with Multiple Personality Disorder. I raised my eyebrows at this at first, but when I stopped to think about it I realized that's a legitimate possibility for Butters's future self. There's some great character development, fantastic action sequences, and it's kind of fun to see what the characters might be like 7 years in the future.
That said, it isn't perfect. About halfway through the authors (This has two authors, and I'm pretty sure they're both female) turn Stan and Kyle into a gay couple. That itself isn't what bugs me, it's the paragraphs on paragraphs of them making out and cuddling that contribute nothing to the story. Whenever a fanfic writer does this, I always feel like I'm reading their personal soft porn collection. To be fair, there are a few scenes like this with a straight couple, but I swear they aren't as numerous or long. I don't even think they go into as much detail. Either way, none of this really felt necessary to me.
But don't let that turn you away, I said this was the best entry on my list and I damn well mean it. Oh, and keep in mind that this is loooooong. This could easily count as two or three actual books. Try reading the first chapter or two and see if you like it. Also, keep in mind that despite being a South Park fic, this isn't meant to be funny. That's not to say there aren't some funny moments, just don't expect to be laughing constantly.
