Current Great Houses:

House Arryn, rulers of the Vale of Arryn from the castle of the Eyrie.
House Baratheon, the Seven Kingdoms royal house, currently divided into two main branches:
House Baratheon of King's Landing, rulers of the Crownlands from the castle of the Red Keep in King's Landing, and the de-facto royal house.
House Baratheon of Dragonstone, rulers of the Stormlands from the castle of Dragonstone, claiming the Iron Throne.
House Bolton, rulers of the North from the castle of the Dreadfort.
House Baelish, rulers of the Riverlands from the castle of Harrenhal.
House Frey of the Twins had hoped to be elevated as the new Lords Paramount of the Riverlands, but were snubbed by the Lannisters in favor of Petyr Baelish.
House Greyjoy, rulers of the Iron Islands from the castle of Pyke.
House Lannister, rulers of the Westerlands from the castle of Casterly Rock.
House Martell, rulers of Dorne from the castle of Sunspear.
House Tyrell, rulers of the Reach from the castle of Highgarden.

Exiled Great Houses

House Stark, the former rulers of the North, ruling from the now sacked castle of Winterfell, until the Red Wedding.
House Targaryen, the former royal house, currently in exile following Robert's Rebellion.
House Tully, the former rulers of the Riverlands, until the Red Wedding.
Extinct Great HousesEdit

Only three Great Houses have ever gone extinct, all as a result of their defeat in the Targaryen Conquest three hundred years before the War of the Five Kings:

House Durrendon - rulers of the Stormlands. Orys Baratheon, founder of House Baratheon, married the daughter of the last king of House Durrendon, thus House Baratheon descends from the Durrendons through the female line..
House Gardener - rulers of the Reach. House Tyrell claims descent from House Gardener through the female line, and House Florent is actually a cadet branch of House Gardener, with a better claim to rule based on lineage than the Tyrells.Several other Houses from the Reach also descend from House Gardener.
House Hoare - rulers of the Iron Islands and (through conquest) the Riverlands. After their defeat, Aegon Targaryen commanded the ironborn to select a new family from among their number to rule over the rest, under the Targaryens. They selected House Greyjoy.