Pathfinder, which I didn't see on your list, also has rules for running organizations. The kingdom-building rules were originally published in the Kingmaker Adventure Path, and were later revised and included in the hardback Ultimate Campaign. That book also contains rules for other types of organizations, mostly structured around creating a base of operations with rooms and equipment and such, and staffing it with teams of workers.
I don't know whether the rules are any good (I bought Ultimate Campaign when it came out, but I've never tried to play with any of the systems). But Kingmaker was an extremely popular adventure path for a long time.