I think that every manga ( shonen , shojo or seinen) have his legal or criminal or whatever kind of organisations , i don't know all the organisations among the mangas because i don't read all the mangas ; since everybody reads different kind of manga , we all knows about many different organisations .
I try to have a general idea because i love organisations or groups in the mangas , it make things a lot more interesting .
Here are those i can think about :
Marine ( one piece)
7 warlords ( one piece)
4 emperors ( one piece)
baroque works (op)
gotei 13 (bleach)
brain trust (get backer)
the empire (rave)
millenion ( gungrave)
the family (gungrave )
the jujinshu ( flame of recca )
There are a lot more i don't remember … add the ones you knows ^^!