When creating a larger world for stories that not only focus on the protagonists and antagonists themselves but also deal with the way those protagonists interact with the world around, one very important aspect are usually the major power groups who are involved in the various great conflicts that are shaping the setting. Similar to how it is quite easy to make an interesting villain, it’s usually not very difficult to come up with dozens of factions that have some nefarious goals. There are plenty of examples in fiction from political conspiracies, demonic cults, criminal organizations, societies of sorcerers, megacorporations, legions of hell, the loyal warriors of a charismatic warlord, and so on and on and on. Creating bad guy groups is easy.
However, when it comes to creating the good guys of a new setting, things very quickly get much more difficult. One big reason for that is that heroes and heroic organizations are stepping on each others toes. If the hero starts out as a small guy who doesn’t know about the big threat of the story when it begins, but the organization is well informed and equipped, what do they need the hero for? They should be able to deal with the problem themselves. On the other hand, if the hero himself is really powerful and capable, then what are the members of the organization to do? Cheer while the hero does his hero thing? In either case, the hero and the heroic organization don’t really need each other. The only way to avoid that is to have the protagonist already be a long time member of the heroic organization and be the best guy they have. Someone like Buffy, Hellboy, or the Master Chief. That can work quite well for books and movies, but for a roleplaying game campaign setting you usually want to have a variety of such groups the heroes can encounter during their adventures and have dealings with.
When it comes to looking at precedents from fiction that could be used as templates for a heroic organization, there isn’t a lot to find either. Usually what you get are either Paladins, Rangers, or the Old Men Council. Paladin type organizations are elite groups of warriors who fight evil in the open and destroy it. Jedi, the Knights of the Round Table, Specters, or the Grey Wardens are example of that. Ranger type organizations are also elite warriors and other agents who sneak around in the shadows gathering intelligence and sabotaging the enemies efforts to provide the forces of Good with information and time to organize a defense against that threat. There’s of course the Dunedain from The Lord of the Rings, but also the Harpers from the Forgotten Realms, or Foxhound from Metal Gear Solid. And of course the Old Men Councils, which quite often are actually Old Women Councils in recent decades. Organizations, often quite ancient, consisting of wealthy philantropist or wizards who manipulate things from the behind the scenes to further the good of all humankind. Only the Old Men Council really has any need for outside help as they usually rely on freelance contractors to do all their dirty work, but that usually ends with the protagonist being a puppet in their plans which doesn’t really need to understand their greater plans. There are also Rebells, but they usually have a single goal which makes them too narrow to be interesting in worldbuilding unless the whole setting is about that rebellion. These rganizations can be employers, but rarely make for good allies. And almost always they mainly exist to deal with one very specific villain organization, which limits their possible uses for other storylines. With a single book or movie, or even three or four, that’s not necessarily a problem, but when you want to create a larger universe for multiple storylines, it’s not really a good solution. As much as I like Star Wars, always having the Jedi fighting the Sith gets stale eventually. Both groups need more goals and ideals than to just oppose each other.
My advice to creating organizations to oppose the villain factions is not to attempt to make Good organizations, but simply non-Evil organizations. It’s terribly difficult to create a well though out God faction, and most of the times they do appear, it eventually turns out that they have not been everything they claimed to be after all. Best case scenario is that they are well meaning, but actually misguided and the protagonist only works with them because he really needs their resources. “I’m not doing it for you, but for the people out there who need my help!” Because most writers understand that truly pure goody-two-shoes groups are boring and often annoying.
When you try to think of truly Good organizations from world history that didn’t do anything shady and cruel, you usually only end up with pacifist groups like the Red Cross or other charities. And unfortunately for fiction writers, especially fantasy and sci-fi, pacifist charities usually don’t pick up arms in battle against evil. Great as they might be, they are not really helping here as examples for Good organizations in adventure fiction.
So I say: Don’t try. What you need is not organizations that do hero work (which they always would do much better then the heroes), but organizations whose goals are serving their own interest, while following ideals that oppose the methods of real villains. Make groups that don’t want to fight Evil everywher all the time, but groups whose goals frequently line up with those of heroic protagonists. We’ve all seen evil Megacorporations a thousand times, who exploit the poor and destroy the environment for profit and sell all kinds of horrible inventions to the highest bidder. But big businesses don’t all have to be Umbrella or Wayland-Yutani. Take for example a big corporation that is heavily investing in colonizing different worlds because they want to get a foothold in alien markets. Their goal is still profit, but their strategy is to build stable local economies and create goodwill with the regional alien governments and companies. They would have a genuine interest to hire mercenaries or cooperate with groups that are already trying to fight pirates, slavers, and hordes of alien locust. They want the region to be safe and their employees to be happy. Not just out of charity, but because that’s also part of their business. Or a group that sponsors expeditions to ancient ruins for the search for old technology or magic. Not to protect the world from the possible dangers if they fall into the wrong hands, but to study them and improve their own creations. They might be quite willing to cooperate with the heroes in finding a certain dangerous artifact, if in turn they get to salvage all the other stuff they might find in that place.
Just like there are no organizations in the real world that want to do Evil, there are relatively few that exist simply to do Good, on the great global stage. (Of course there are plenty of charities, but how often do you see any of those mentioned in history books other than the Red Cross?) They all have much more complex goals and causes they are pursuing. So instead ask yourself, what kinds of groups would benefit from cooperating with heroes in this fictional universe. I think this always gets much more interesting results. It won’t work for any nonsensical Hollywood/America saves the world plot where the hero blows up Nazi aliens, but you might notice that those are usually one-shot movies anyway, because the premise is so weak that there isn’t really any worldbuilding for the greater world beyond the hero at all.