I got a big load of ideas for organizations, which I'd like to share before I start to go deeper them.

Criminal Organizations
The Blue Sails: One of the oldest and largest criminal organization of the Barbarian Lands. The Blue Sails are an extensive network of smugglers who are opperating from the elven islands of the Inner Sea. The transport and trade in almost anything nonliving, but make occasional exceptions for rare magical animals or anyone who needs secret passage and is willing to pay abhorently high prices for that. The Blue Sails don't have anything to do with assassinations, kidnapping, or burglaries, and use blackmail mostly to keep their own business running. In rare cases they hire themselves out to board ships out on the open sea to retrieve valuable artifacts or prisoners, but outright piracy is not among their activities.
In the elven islands, the Blue Sails are not as much a band or criminals, but an established institution. It's no problem at all finding the local leader of the group by simply asking dockworkers or shopkeepers and as long as they pay their docking fees (plus some) the guards don't bother them. On the mainland they are more descrete and avoid being noticed by the local authorities. In the islands, the Sails have contacts throughout the nobility and merchant houses and only the most dangerous or daring pirated ever attack their ships.
The Hidden: The Hidden are a network of Vandren thieves and other rogues that are believed to have existed even before their migration to the Barbarian Lands. Werever Vandren are living in significant numbers, the Hidden have some of their men as well. In the early decades, they had used their connections to arrange certain secret agreements and performed other services for the chieftains who were trying to find a new foothold in the Southern Clanlands. When Vandren fall on hard times, the Hidden are often near to offer their assistance, and many of those debts are still being paid off to this very day.
The Hidden are easily the largest and most powerful human criminal organization. They compete with the Blue Sails for the trade with goods that are forbidden in Vandren ports and are making a fortune with selling their services to powerful people who really only need them because they started to accept such offers many years ago. To lots of people, the Hidden are parasites who only cause much more trouble than what few good they are doing. The Hidden usually stay away from such people, as they lack the manpower to defend themselves against chieftains who bring all their warriors to crack down on them. Instead they are perfectly content to wait for opportunities in which only they can help and then make sure that the person in charge would never risk to move openly against them. The numbers of the Hidden probably range into the thousands, but most are just ordinary people who keep their eyes and ears open and arrange for certain people metting each other and certain packages reach their destination.
The Nightcloaks: Any time someone is speaking of the Thieves Guild, it is usually the Nightcloaks who are meant. The Nightcloaks are a powerful group of thieves who opperate throughout all of the elven clanland. They also deal in smuggling, extortion, counterfeiting, and the occasional assassinations and there is almost nothing they wouldn't do as long as they can keep a relatively low profile in public.
Smugglers Cove: Smugglers Cove is a small rock in the Inner Sea that really consists only of barren cliffs and a single harbor. It lies close to several of the major trade routes and only a short detour for most ships, but almost all merchants try to stay clear of the island unless absolutely neccessary. Smugglers cove is relatively small, but one of the few ports that is not controled by any of the major clans and completely neutral. It's proximity to many trade routes makes it a very attractiv destination for pirates and anyone who wants to disappear for a few months. While the town does not have any real government, it's almost entirely controlled by a dark elven rogues and her gang. She owns the entire docks and warehouses and all of the inns, taverns, and shops pay her a hefty amount of money for the previlege of being allowed to stay. While the current owner has been on the island for almost 70 years, the town itself is much older and had been used by pirates long before the Vandren came to the Barbarian Lands. While only a small fish when compared to the other criminal organizations and not doing any business on the mainland or the elven islands, the elf and her gang are one of the major criminal groups since almost anyone who needs a safe harbor to repair and resupply away from the major port needs to come to her. And non of the pirates and smugglers of Smugglers Cove have any interest in seeing major fighting destroying the town.
The Talons: The Talons are a small group of assassins, drug, and poison smuglers, who have shown up in the northeastern parts of the Southern Clanlands only during the recent decade. They consist mostly of elves and tiefliengs, and rumors say they are led by a true demon. Their longterm goals are unclear, but they have started to cause a lot of trouble to the Blue Sails and Nightcloaks.

Magical Organizations
The Black Tower: The Black Tower is a society of elven, human, and gnome sorcerer which is based in a tall keep of the same name near the road that connects the Northern and the Southern Clanlands. Black Tower agents travel throughout the clanlands, keeping their eyes and ears open for signs of threats that may be of significant danger for the civilized lands and try to keep the regional chieftains aware of major threats that go beyond the regular inter-clan sruggles.
The Dark Ones:The Dark Ones are an unusual organization in that they consist almost entirely of a single dark elven clan of Endarei. Like the Keiyashei tribe, the Dark Ones prefer to live underground in a large cave city but are unique in that all their shamans are also shadow mages. The shamans are in the service of Ancients, but nobody knows why the entire clan has entered the pact and what the purpose of all is.
The Demon Hunters: The Demon Hunters are an order of warriors and sorcerers trained to find and destroy warlocks. Most members are humans and they are commanded by one of the six guardians who rule over the Crystal Caves. Their opposition to anyone dabbling in demonic magic naturally has them at odds with the Magic Seekers, who have their main area of influence just a few hundred miles to the North.
The Magic Seekers: The Magic Seekers are a society of elven sorcerers and nobles that is dedicated both to the pursuit of magical discoveries as well as the elevation of wood elves to greater power through magic. Though more an informal network of like minded individuals than an actual alliance or confederation, the society includes many very powerful and influential people among its upper ranks as is increasingly becomming the dominant power in the eastern parts of the Southern Clanlands. The organization also have many members and sympathizers in the elven islands, but their influence over politics is much less extensive there.
Many of the Magic Seekers believe that conventional magic is just a small part of what magic really has to offer and perform extensive research in void magic, which puts them in opposition with the Demon Hunters and doesn't make them any friends with many elven shaman groups.
The Shadow Society: The Shadow Society is a group of sorcerer mystics who have devoted themselves to discover the hidden nature of the Shadow World. Their studies and research often have them on the hunt for rare tomes and items and they descretly contact scholars and chieftains all over the northern Barbarian Lands. Their searches often lead them to the possession of many ancient and lost secrets, which they use to bargain for whatever it is they wish to acquire. While not a nefarious organization, members of the Shadow Society often sweeten the deals they offer by also promissing their silence in regard to certain things their business partners would rather be kept secret.
Void Keep The Void Keep is a castle of magnificent size that is located on an island just off the coast at the very north of the Inner Sea where it opens into the Frozen Sea. The remote location far from any major port makes the Keep relatively obscure, but it is infamous for being almost entirely inhabited by tieflings. The keeps population numbers about 1,000 and the relative uniformity of their demonic features makes it likely that they migrated from the Void in a single group and are not made up of tieflings from all over the Barbarian Lands who have simply gathered in a single place.