Okay well to try and drag this topic slightly back on track after helping derail it a bit myself here's a list of some of the canon intelligence agencies in Shadowrun. They're all from Third Edition sourcebooks but I don't think that should be too much of a problem. Now I've probably forgotten or missed some but I'm sure some of the other posters can fill in the gaps. A lot of credit for this goes to Raygun and all the posters from the Intelligence Agencies thread I started a few years back that helped contribute.
National Intelligence Agencies
North America
UCAS - Army Intelligence
UCAS - Central Intelligence Agency (CIA)
UCAS - Defense Intelligence Agency (DIA)
UCAS - National Reconnaissance Office (NRO)
UCAS - National Security Agency (NSA)
CAS - Department of Strategic Intelligence (DSI)
CAS - Department of Domestic Investigation (DDI)
CAS - Extraterritoriality Registry and Liaison Agency (ERLA)
Tir Tairngire - Information Secretariat (IS)
Sioux - Office Military Intelligence (OMI)
Sioux - The Matrix Warband
Cuba - Dirección General de Inteligencia (DGI)
South America
Amazonia - Departamento de Inteligencia e Seguranca Amazonica
Europe
AGS - Argus*
AGS - Bundesamt für die Innere Sicherheit (BIS)
Russia - Upravleniye Gosudarstvennoy Bezopasnosti (UGB)
Russia - Glavnoye Razvedovatel’noye Upravleniy (GRU)
Tír Na nÓg - Internal Affairs Registry
UK - Secret Intelligence Service (SIS)
UK - Security Service (SS)
UK - Lord Protector's Office aka. The Templars
Papal States/Vatican - Vigilia Evangelica
Middle East
Israel - HaMossad leModi'in v'leTafkidim Meyuhadim (Mossad)
Israel - Shin Bet
Asia
Japan - Japanese Intelligence Agency
Japan - Imperial Household Agency (IHA)
Japan - Chobetsu
Australia - Australian Intelligence and Security Enforcement (AISE)
Shaangxi - Wanguo Anbu
Henan - Ministry of Internal Security (MIS)
Korea - National Intelligence Service
Javanese Republic - 'Javanese intelligence' (Reference only, no name known)
Corporate - Private
Cross Applied Technologies - Seraphim
Shiawase - Market Intelligence and Forecasting Department (MIFD)
Yamatetsu - Yamatetsu Naval Intelligence
Yamatetsu - Special Security Detail (SSD)
MET 2000 - Argus*
Ares - Knight Errant Intelligence
Ares - AreSpace
Saeder-Krupp - S-K Prime
Corporate - Free Market (The guys Joe Public can hire to do stuff for him unlike private corporate organisations)
The Market Research Group (MRG)
Aegis Cognito
Infolio
Esprit
10,000 Daggers
Other
Corporate Court Crisis Coordination Committee (C5)
Grid Overwatch Division (GOD)
*Argus is a weird case in that it's the intelligence arm of MET 2000 that hires itself out so as well as being the main AGS intelligence agency from what I can see it kinda falls under all three categories of national, corporate - private and corporate - free market.