There are a variety of organisations and secret societies in Broken World, and this is a brief explanation of a variety of them. This is a work in progress, and is not a complete list.
Whilst it is true that every government might have spies and military, they are only mentioned here if there is something interesting or exceptional about them.
Astorina Ultima: This organisation is founded on the principle that the breaking could have been avoided if the rest of humanity and other races were united under Imperial rule. They work in all ways towards a restoration of the Imperium. It is not officially part of the government, but has the approval of the Astori themselves, and many resources from government coffers.
Sesthas'nar: This organisation is a joint venture between Sytheria and Sytheros. It is a research council that seeks to find a way to increase the Ophiduan birth rate.
Quesaran Unity: This organisation fosters continued cooperation between the three subcultures to prevent any tension between them. They work to ensure that Quesaras remains united and strong.
Druid Circles and Ranger Orders:
Each of these organisations is split into 2 allied groups. The druids refer to themselves as being in "Circles" and rangers prefer the term "Orders". Each is an allied but independent organisation that works to a common goal. Though some groups have common ground, many are opposed ideologically and come into conflict
Shepherds: This organisation sees itself as the stewards of the new world, and seek to help the world adjust. They guide outsiders to the best ways to farm and forage, as well as to be sustainable so that no-one starves.
Restoration: This organisation seeks to reverse the breaking as best they can. They hunt down the mutated beasts and try to heal the lands back to their original state.
Claw and fang: this organisation works to ensure that the wilds recover and flourish. They see the god's curse as a blessing, as it means that only the strongest will survive.
Storm's callers: This organisation seeks to unleash the wildest rages of the weather. Whilst the Circle is strong, few rangers join the Order.
Hunters: This organisation has many rangers in the order, and a few druids in the Circle. They seek to hunt not just for food, but also for sport.
Sky Stewards: This organisation hires itself out to any that can pay. They control the weather for profit. Rangers of this order protect the druids that can control the weather, acting as bodyguards.
Renewers: Despite a name that sounds quite positive, this organisation believes that the breaking did not go far enough, and that the world should be remade anew. They seek to have nations fall and society crumble, and for nature to reclaim the world. Many governments consider them a terrorist organisation.
Thehn homecoming: This dwarven organisation seeks to find a way to reclaim Thehn from the vicious undead. They yearn for a return of a Dwarven homeland, and a cloistered life.
Elan Council: The Elan council determines candidates to be reborn into their race after they die or are near death. They also work to keep the existence of their race a secret as much as possible.
The Swarm: This multi race pact is founded on a single principle: All sentient races should be joined into a single Hive-mind like the dromite once were, so that this unified mind can live in peace and harmony, exploring the limits of true psionic power. To many, this organisation comes across as a cult, and it is illegal in the Imperium to espouse their philosophy.
The Guild of Psionics: this powerful guild crafts and sells psionic items, as well as researching psionic powers and developing new items for use. Most medium to large sized towns have a Guild house that also doubles as a trading hall.
The Guild of Hospitalers: This guild focuses on those that can heal the body and mind, whether through psionics, divine magic or mundane skill. Though it will use divine power, the guild distances itself from the gods at all times to ensure there is no hint of religion. They sell their skills and healing items, having a slight rivalry with the guild of psionics.
Society of Wardens: This organisation works to root out cults to the divine, and opposes the machinations of the echo gods. It is supported unofficially by many governments, and has members from all races.