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)
World governement(OP)
revolutionist(op)
baroque works (op)
cipher pol(op)
akatsuki(naruto)
gotei 13 (bleach)
espada (bleach)
brain trust (get backer)
oration seis(rave)
demon card(rave)
six guards(rave)
the empire (rave)
hellsing (hellsing)
vatican(hellsing)
millenium (hellsing)
millenion ( gungrave)
the family (gungrave )
the jujinshu ( flame of recca )
There are a lot more i don't remember … add the ones you knows ^^!