Yeah, it's hard to track some of them down (Which is, well, kinda the point, secret and all!), but there are a few that are bigger players than others. Interestingly, they're all magic based. Off the top of my head:
The Black Lodge
Possibly once-connected to the Catholic Church, the Black Lodge are a group of magicians with a secret order, black robes, chanting in Latin, and are based in Europe. They're up to something but nobody really knows what. They have members in old UCAS and CAS aristocracy.
The Initiates of the New Dawn want to bring a glorious revolution where magic is in everyone's hands and the Awakened world is accepted as the new norm. They're much more public than most groupssince their agenda is, you know, magic for everybody.
I've never eally figured out what the Apep Consortium is doing.
The Dunklezhan Institute of Magic (DIMR) is doing Stuff and will probably be opened up some in Clutch of Dragons (Out soon!)
The Atlantean Foundation is a private group founded by a woman in Atlanta whose name escapes me, but is a false identity for an Immortal Elf. Her people have been searching for old magical artifacts, whichputs her head to head with bunches of other secret arcane groups.
The Immortal Elves (IEs), all have their own private agenda. The formations of Tir Tangaire and Tir na Nog were two of these, but both are a tad shakey these days.
The Great Dragons all have their agents.
The Smoking Mirror is the Aztechnolgy blood magic cult that wants to bring the Horrors back. They've taken some big hits over the past few years.
I'm forgetting a few. James will probably be along in a while to drop somemajor data on us. Chummer's a walking encyclopedia of Shaowrunology and I'm always damned impressed by him.
There's really quite a lot of them.