Starfleet: House Stark
The Maquis: House Greyjoy
The Cardassians: House Lannister 
The Klingons: Dothraki (duh)
Bajor: House Tulley?
The Dominion: White walkers/others
Parwraiths: House Targarian
Also Tyrion and Garak both say that everything they say is true "Especially the lies"

Does anyone else get a Game of Thrones vibe from Deep Space Nine or, conversely, a Deep Space Nine vibe from Game of Thrones? The complaints in this review about the shortsightedness of any political moves that would kick the federation out of Bajor parallel my own complaints about the Game of Thrones characters…

Blood and Roses from Orxy and Crake by Margaret Atwood. It's an imbalanced computer game that has players trading off human atrocities against signs of human progress/greatness. The player who plays the blood/atrocity side always wins because it's not a mario game