Master list of Fanfiction index

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Fandom

2PM (K-pop/K-r&b)

Angelic Layer (manga)

Bakuten Shoot Beyblade (anime, first 3 seasons)
Boushiya Ellipsis (manga)
Boys over Flowers (K-drama)

Card Captor Sakura (anime, manga)
Combination (manga)

Detective Conan (anime, manga)
Digimon (anime, all first 4 seasons)
Dong Bang Shin Ki (TVXQ/Tohoshinki) (K-pop/J-pop)

Fairy Tail (anime, manga)
Flame (J-pop)

Gate 7 (manga)
Gohou Drug (manga)
Gundam Seed (anime)
Gundam Wing (anime)

He's a Naturalist (manga)
Horitsuba (manga, CLAMP verse)
Hunter x Hunter (anime)

Initial D (anime)

Kamen Rider W (J-drama)
Katekyouishi Hitman Reborn! (anime, manga)
Kingdom Hearts (game)
Kobato. (anime, manga)
Komatta toki ni wa hoshi ni kike (manga)

La Corda d'Oro (anime, manga)
Lead (J-pop)

Magic Knights Rayearth (anime, manga)
Mimi wo Sumesaba (anime)

Naruto (anime, manga)
Natsume Yuujinchou (anime, manga)

One Piece (anime, manga)
Only the Ring finger knows (manga)
Only Yesterday (anime)

RG Veda (anime, manga, music video)
Rin! (manga) 

Saint Seiya (anime)
SHINee (K-pop)
Super Junior (K-pop)

Tennis no Oujisama (anime)
Tsubasa RESERVoir ChRoNiCLES (anime, manga)
Tokyo Babylon (OAV, manga)

Vocaloid (other, music video)

Weiss Kreuz (anime)
w-inds. (J-pop)

xxxholic (anime, manga)

Yami no Matsuei (anime, manga)
You're Under Arrest (anime, first season)
Yumeiro Pâtissière (anime)
Yuu Yuu Hakusho (anime)
Yuugiou (anime, mostly the first season)