Are there a Secret Societies or Factions hiding in your World? Tell me about one!
Just acknowledging that there's a secret faction, wouldn't make it secret anymore. It's the first rule of secret societies: We don't talk about our secret society.
Herein also lies a little bit of a problem. You can't have a truly secret society, were nobody knows they exist, who belongs to it or what they do. Because then nobody is looking for them. When something happens it needs to be attributed to somebody or something. In the end it will boil down to Landmark, Hidden, Secret and what I have talked about factions in the past.
You could argue, that maybe people have wrongly attributed some actions to somebody but in fact it was actually a secret faction all along. But that faction wouldn't still be a true secret faction. I know their goal but not their identity. Even if you can figure out a truly secret faction, it wouldn't be much fun playing with it. There's nothing to interact or roleplay, so why bother?
So, no there are no secret factions in my world(s). There are factions and groups with varying secrecy.
Having said that, I'm intrigued by Observers from the TV-Show Fringe. Just some people that hang around an just observe what happens. Not to go into too much detail and spoilers here, yes, they had an ulterior motive for doing so. But I could imagine just a faction that does record events and stores them away, nothing evil or good. Just observing. It's kind of meta, since you could imagine, that you as a player could be such an Observer, that experiences and records events through the eyes of your characters.
So, maybe there's a secret faction. And it's the players.