The Black Chamber: Probably the most well known and infamous. The Chamber has no problem with the existence of monsters – many native to this world it reality – and recognize them as part of the ecosystem. But even so they take steps to limit their populations via the execution of breeding pairs. They are very good at hunting and exterminating monsters as well as hiding their existence be from the world at large.
CASPER (Centre for Secure Poltergeist Elimination Research): A branch of the Department of Education, CASPER exists to convince the public that ghosts don’t exist. And do this by means of exorcisms on ghosts as well as disinformation campaigns.
The Montauk Project: Time travel experiments gone wrong. It was founded(?) in the 1940’s and source of the Manhattan Project, though most stories about it don’t begin until the 1980s.
At least 70% of the time it does not exist.
The Border Patrol: There are more attempted incursions into the universe from Outside than most know. Not everyone is met by one with the power to meet such things. For the rest, there is the border patrol. They are THE elite if secret agencies and generally the only one magicians respect. Every other agency is technically at their beck and call. If you need anything done efficiently and violetly, they are the only number you need to call.
Their attrition rate of members is a thing of legend.
The Metric Board/Commission: A little-known agency who police various magical talents in Canada and the United States. It’s rumoured that they kill more humans than any other agency and other agencies consider them a newcomer to the field and a poorly-run one at that. They are rare in operating jointly in two countries at once.
Sister Eye: A satellite system and providers of data to whomever requires it. They have access to alien tech, satellites only they know about and can actually detect some fae glamours, which is pretty much their claim to fame. A very minor player, but a useful one.
Homeworld Security: An umbrella UN group with global leverage, they oversee all other secret agencies and, as the name implies, are charged with keeping Earth secure. This is largely done by allocating resources to other agencies as needed.
MK Ultra: One of several names (Illuminati etc.) given to an organization that tried to hide weird shit from humanity via telepathic tricks, etc. The rise of the internet pretty much put an end to it and the organization was mostly folded into other ones.
The Deep School: A school that exists to teach creatures from Outside the universe about it and how to fit in/disguise themselves. Who founded it and what its overall motives for are unknown but they do supply ‘experts’ to agencies if needed and do aid in destroying Outsiders who break their rules.