There are five major noble houses, or Royal Houses, and a dozen or so minor houses.  House Justinian used to be a major house but fell in status. In addition, the Houses of Alecto, Gesar, and Windsor were left extinct after the First Emperor War. House Chauki is also believed to be extinct, overthrown by the Hazat.
Royal Houses

Al Malik: The exotic and inscrutable al-Malik are often accused of being mere merchants, for their ties to the League are well known.  But they have proven their noble legerdemain many times, through the acquisition of land and a unique understanding of human nature and politics.  It is very hard to pull one over on an al-Malik, but it is likewise hard for them to resist the lure of a good adventure or challenge.  Vassals of this family are well-treated and return the respect with solid service.

Decados: Slimy, cunning and extremely successful, the Decados have risen to power through treachery and an uncanny understanding of their rivals helped in no small part, no doubt, by their vast, invisible intelligence network. While the other families accuse them of a number of crimes, the Decados are here to stay and thus must be dealt with on their own terms. Decados vassals despise their lords but are kept in line through fear or the promise of power for those who make good quislings.
Hawkwood: Prideful yet honorable, the Hawkwoods have seen one of their own take the Emperor's throne.  While Alexius Hawkwood has since distanced himself from his family to appear more impartial, the Hawkwoods take such political setbacks with stoicism the same fierce perseverance with which they beat back the barbarian raiders to their worlds.  A Hawkwood does not give up.  House Hawkwood is more beloved by its vassals than any other house, for they treat them fairly and with justice.
Hazat: Hot-blooded and intense, the martial Hazat know how to field an army but are also no strangers to intrigue. When they can calm the vicious infighting from family to family, they can present a formidable front against rivals from other houses. Left with less land after the wars than they began with, they now pursue a campaign against a barbarian world, seeking new lands outside of the Empire.  Hazat vassals are loyal, for they know that sacrifices for their lords are often rewarded.
Li Halan: This pious and disciplined family was once the worst behaved of all nobles.  Their immoral exploits are legendary, as is the tale of their overnight conversion to the Church.  They now pursue the scriptures as fanatically as they once chased pleasure.  While other nobles may snicker at the faithful lords, they more often fear the Li Halan, for this family has proved implacable on both the battlefield and at court.  Their vassals are fiercely loyal, for they know their place as vassals in the Pancreator's plan.
Minor Houses

Cameton: House Cameton's  holdings are limited to Byzantium Secundus, where they assume a sort of stewardship of the Empire - and are less than pleased to have an actual Emperor on the throne these days.  Arrogant, greedy, and insincere, they usually become diplomats or administrators, the better to serve their own interests. 

Chauki: Not really a minor house, but a former Royal House that was supposedly exterminated.  Their remnants survive on the Lost World of Iver, accessible only through the second, secret jumpgate at the outskirts of the Pandemonium system.  Claiming to be from House Chauki is like painting a large red target on one's forehead the Hazat in particular would be happy to silence you.

Juandastaas: This house leaves many uneasy; it is the most friendly to aliens, and particularly to Ur-Obun.  To this day, mixed marriages between Juandastaas nobles and Obun and not uncommon.  During the days of the Second Republic, some of its members even used genetic manipulation to make such unions fertile, thus introducing alien genes in the house's line.  The Juandaastas are open-minded and even-handed, tending towards philosophy and diplomacy.  They are fierce advocates of alien rights, and have a high incidence of psychic ability. 

Justinian: Loyal and honorable to a fault, this martial house stood by House Alecto even as it was destroyed, and lost their primary holding, the world of Paradise, when the jumpgate mysteriously sealed.  Their house is now divided between a conservative Old Guard, and an aggressive band of Young Turks. 

Keddah: The only minor house that claims rulership of a planet, Grail, home of an important Sanctuary Aeon monastery and site of the Prophet's Healing, and is thus wealthy.  Bound by an ancient treaty to the hated Decados who force them to war with the Al-Malik.

Masseri: The poorest, most destitute of the noble houses, it used to hold dominion over the planet of Daishan but lost everything in the Symbiot invasion.  It is now beholden to the Decados, who never let anyone forget it.  Many of members of the younger generation of House Masseri have renounced their heritage instead and are now seeking their fortune as freelancers.

Shelit: A mysterious house of disfavored Kurgan nobility, the Shelit have allied themselves with the Hazat against their Caliphate rulers.  Ultra-rational, dispassionate, conservative, and low in profile, they are cybernetic engineers without peer, and all have at least one cybernetic limb. 

Thana: Engineered with tall, slender physiques, almost avian - yet beautiful - bone structures, violet eyes, and translucent hair, the Thana ruled Eridol before the beast-like Aluun drove them away, and the jumpgate sealed.  Disdainful, long-lived, and highly psychic, but scholarly and artistic in nature, they were at one point controlled and carefully watched, but now serve many noble patrons.  The Church keeps a close eye on them.

Torenson:   Reputed for their sense of etiquette and skillful management, many younger scions of House Torenson act as seneschals or chaimberlains for other noble houses.  Authorities on noble mores, manners, and etiquette, House Torenson is slowly gathering influence again as many of its nobles act as social advisors to nobles of the Royal Houses.  Strict, rigid, they are unswervingly neutral in all matters save social grace. 

Trusnikron: A young, energetic house, Trusnikron is deeply honorable, straightforward, and self-reliant.  Trusnikron are superior cavalry and animal trainers, serving House Hawkwood as cavalry officers, and the Hazat as mercenaries.  They have little political skill, and are considered uncouth and barbaric by most other nobles. 

Van Gelder: Once all but ruined, the Van Gelder owe their survival to the Decados, who they now serve as spies and assassins.  Bitter, angry, and solemn, they are untrusting, lack any regard for honor, and have a talent for poisoning.  The Decados provide them with many riches, but only so long as they remain useful. 

Xanthippe: The Xanthippe seldom have their holdings planet-side, preferring space stations and starships.  A small, matriarchal house, the Xanthippe are canny and tough, with a reputation for producing fine wine, and elite mercenaries.  In general, female Xanthippe become leaders and warriors, while male Xanthippe become artisans, and healers.  All of their lore and law is contained in a text called the "Measure".