Fanfics I read/have read

Harry Potter:
Harry Potter and the Methods of Rationality -- Eliezer Yudkowsky aka LessWrong
Significant Digits -- /u/mrphaeton
Hogwarts Battle School -- Kwan Li
Seventh Horcrux -- Emerald Ashes
Ruthless -- AngelaStarCat

Naruto:
Time Braid -- ShaperV
Indomitable -- ShaperV
The Waves Arisen -- Wertifloke
Team Anko -- Eaglejarl
Roll the Dice on Fate -- jackercracks

Avatar: The Last Airbender
Embers -- Vathara

Dungeons and Dragons:
The Two-Year Emperor -- Eaglejarl (no longer available)

Worm:
Time of Perils -- Ouri Maler aka sun tzu

Superman:
Metropolitan Man -- Alexander Wales

Twilight:
Luminosity -- Alicorn

Harry Potter and the Natural 20 (D&D x HP) -- Sir Poley

Also, most of what gets recommended on /r/rational.