Cult of the Undying Wyrm - A secretive cult revolving around a shadowy leader, supposedly a great Dragon of the Prophecy seeking to become a god using The Fiendstone as detailed in the prophecy.
Eternal Cogs - A guild/cult of engineers who believe Magic is too unreliable and that the future is in mechanical contraptions. The Twelve is extremely hostile towards them, and so they operate out of the underground, performing backdoor deals with national weapons suppliers and procurement officers.
Long Arm - A monastic Order; important to the Point of Infinity campaign.
The dragonmarked houses are independant of nations and hold tremendous sway over them regardless. Players can apply for membership to any of the houses, but may not belong to more than one at a time, at least not openly. Houses often are interconnected, such as House Cannith and Orien both inventing the Lightning Rail, and so working with eachother is encouraged.
House Cannith - Human Mark of Making
House Deneith - Human Mark of Protection
House Ghallanda - Halfling Mark of Hospitality
House Jorasco - Halfling Mark of Healing
House Kundarak - Dwarf Mark of Warding
House Lyrandar - Half-elf Mark of Storm
House Medani - Half-elf Mark of Detection
House Orien - Human Mark of Passage
House Phiarlan - Elf Mark of Shadow
House Thuranni - Elf Mark of Shadow
House Sivis - Gnome Mark of Scribing
House Tharashk - Half-Orc Mark of Finding
House Vadalis - Human Mark of Handling
Power of Purity - An association that believes in negotiating with elementals over binding them.
Associated with Marked Houses
Finders Guild - House of Tharashk prospectors and bounty hunters.
Fabricators Guild - Mercantile branch of Cannith, focuses on production
Tinkers Guild -Mercantile branch of Cannith, Focuses on Repair and invention
Blademarks Guild - Mercenary branch of Deneith, Less experienced, not many marked
Defenders Guild - Mercenary branch of Deneith, more expensive, many marked.
Sentinel Marshals - International police force administered by Deneith.
Raincallers Guild - Administered by Lyrandar
Order of the Emerald Claw - A terrorist organization which used to have loyalties to Karrnath
The Aurum - The wealthiest elite in Eberron, seek financial control.
The Blood of Vol - Undead worshipping cult
House Tarkanan - Criminals banded together by the fact that they have Aberrant Dragonmarks.
The Chamber - Dragons who want to take an active interest in the world
Cults of the Dragon Below
The Dreaming Dark - A group of psionics from Riedra who work as the eyes and ears of the Quori
The Lords of Dust - Ancient Demons
The Daelkyr - Ancient Demons
The Cult of Life: Despite its benevolent name, this subsect of the Blood of Vol is filled with some of the most dangerous Seekers in the world. Its members are known as “thieves of life,” and for good reason: The entire purpose of the cult is the pursuit of immortality, paid for with other living souls. Those at the highest levels of the cult are fully aware of their organization’s connection to Vol and often take orders directly from the Crimson Covenant. Neophyte members are kept ignorant of these truths until they have earned their place.
The Hornblade Clan: This confederation of orcs and goblinoids has grown from a small tribe into the single largest community of Seekers on Khorvaire in the time since the end of the Last War. Before the war, the Hornblades were a large orc tribe in western Khorvaire, but they were decimated by infighting with druid cousins who felt they had lost their spiritual way. The clan’s purpose was renewed by the return of a half-breed exile by the name of Janilya. After besting the former chieftain in mortal combat, she united the clan under the banner of Vol and made clear her vision for the future: The Hornblades would allow Seekers of other races to join the tribe, if their belief was strong enough. Since then, the clan’s ranks have swelled with new arrivals (mostly goblins and other orcs) who come to hear the word of their new prophet, to be a part of her vision of unity, and in the case of those found unworthy, to become ritual sacrifices for the good of the community.
The Keepers of Blood: Few cults have caused so large a rift in their parent faiths as have the Keepers. Some Seekers welcome them, while others view them as heretics of the worst order. The Keepers of Blood revere both the principles of Vol and the Dark Six god known as the Keeper. Most cultists do not actually believe in the Keeper as an entity but revere his alleged portfolio. Only by recognizing and revering both primordial aspects can they be assured of divinity or life everlasting. In many ways, they are the most conservative sect of the Blood of Vol.
Others (Academic, Mercenary units etc.)
The Wayfinder Foundation - Funds exploration
Wardens of the Wood - Druidic Organization
Morgrave University - University in Sharn
The Twelve - Arcane scholars of the 12 Dragonmarked families
The Library of Korrenberg - Prestigious Library
Sharn Inquisitive - Sharn's newspaper
Heirs of Dhakaan - Goblinoids wanting to bring back the glory of The Empire of Dhakaan
Church of the Silver Flame
The Gatekeepers - A druidic sect who watches over the seals which bind the daelkyr in Khyber.
The Royal Families
The Serenading Sailors Of Swordkeep