[Jonouchi]

Anime:

Bleach:

Ichigo x Renji/Grimmjow/Keigo
Ikkaku x Keigo

Dragon Ball / Z / GT:

Goku x Gohan/Goten/Yamcha/Jeice*
Burter x Jeice

Eyeshield 21:

Monta x Hiruma x Sena

Fairy Tail:

Natsu x Gray

Gintama:

Hijikata x Gintoki / Sougo
Katsura x Gintoki / Kondo / Elizabeth (Spoiler Note: Elizabeth is a guy.)

InuYasha:

Inuyasha x Kouga
Hakkaku x Jinta

Naruto:

Naruto x Kiba x Shikamaru

One Piece:

Zoro x Luffy / Kaku
Young Franky (Age: 20-ish)* x Zoro / Luffy

Ouran High School Host Club:

Hikaru x Kaoru
Mori x Ritsu

Yu-Gi-Oh!:

Mako x Rex


Video Games:

Final Fantasy IV:

Cecil x Golbez x Kain

Final Fantasy V:

Bartz x Gilgamesh

Final Fantasy VIII:

Zell x Squall / Raijin

Final Fantasy IX:

Zidane x Blank x Marcus

Final Fantasy X:

Tidus x Wakka

Phoenix Wright Series:

Larry* x Tigre* x Shi-Long*

Suikoden I / II:

Viktor x Flik / Rikimaru*
Pahn x Gremio
Chaco x Riou / Sid
Shilo x Yam Koo*

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Put a * next to all of the crack pairings, but they all work in my head to one extent or another.