I have been building game worlds since some time in the 1980s, some organizations have appeared again and again - growing and developing in each iteration. Never let a good company die out, you might need it again later - and you can use all the old PCs and NPCs again - it saves inventing new things each time, is quicker and comes with history, personality and RP opportunity, bringing instant 'flavour'.
FFTC - The Far Flung Trading Company specializes in those local routes and frontier routes that don't interest the larger merchant houses. It started in the 1990s as a vehicle to support The Occidental Trading Company, and has grown to incorporate some of the smaller merchant houses established in games. It is one of the few truly international groups, with members from Hann, Sakar and many of the unaligned states.
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Church of Way - Originally The Brothers of the Way, now the Church of Way, this small church builds bothies and hostels for travellers. The original Way House was built by
Yuthric Green-Teeth, and then grew into a widespread religious organization.
The Amethyst Fist - an order of monks, that started in a NWN world and have been developed for Pathfinder.
The Raven College of Armes - Every game-world needs its honours and titles - The Raven College of Armes has done that since the very first world that I built. It was started by a one of my PCs (turned NPC) druid, as a cross between an early (1st ed) Celtic Druidic/Bardic college with the additional task of recording and verifying titles and coats of arms.
The Golden Billet - A new organization that has only appeared in a couple of games, so far. It provides 'contracted out' protective services to states and organizations. A pure NPC organization.
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Roth - A family concern that is best known for Poachers Pale Ale, Grapes of Roth (red) wine, and Dragon's Breath Schnapps - all of which travel well. They also brew ales and winers for local consumption. Their main business is in the Tusk area, although they are building a new brewing center in The Old Frontier region.