Another axis to look at is the sinister/friendly one. A sinister organization will tend to do things to control the people of which is it a part, whereas the friendly will seek to help it. Although all organizations seek to control and help the people of which is it a part, this addresses which is more important to the organization.
A sinister organization is interested in using whatever power it has to control as much of the group it is part of as possible. Consider how government law-enforcement organizations are treated in cyber-punk: The CIA goes around assassinating public figures that are leading the United States away from military intervention while toppling countries in order to foment chaos among its enemies. The FBI is not just an investigatory agency but regularly arrests those that it sees as saying or doing anything essentially un-American; it is almost as if J. Edgar Hoover never died. These organizations are not just interested in doing their job, but using their power to control how Americans deal with the world.
Friendly organizations, on the other hand, stay in the background. Although it can be argued that they are using more subtle controls, they are there to help the people that they are created by. An example of this is the USDA; although it can be argued that it is a tool of other, more sinister forces, most of the food safety reforms come from the USDA, as well as virtually libraries on almost any agricultural or nutritional topic that can be imagined. It is hard to see the USDA as a sinister in and of itself, and it is usually portrayed either helpful or naïve.
Story-wise, the difference defines how dark or light the universe is. Dark universes are full of sinister organizations, where every organization is full of corrupt leaders doing their best to hold onto whatever power they have, boring administrators doing little more than filling out the necessary paperwork, and highly trained and deadly agents enforcing the will of those organizations. There is a reason why darker worlds rarely focus on more than one organization; although their powers may be different on paper, they are all ultimately of the same dark stripe, and only the name matters. You just need a name to slap on an organization, and you're good.
Friendly organizations, however, are vastly different, and the name is of actual importance. Although an organization may have its enforcement arm, it usually tries to talk someone down, and bland agents are dispatched to investigate the situation first. Eventually the investigation will be completed, and the suspect will either be released or taken into custody. But all of this will be done by the book, and no one will really be offended by the investigation; it is just the agency doing its job.
Of course, there is a neutral position, where organizations just are. They must be dealt with, of course, and provide for some nice conflicts, such as dealing with the Department of Motor Vehicles to get a license, but that's no fun. Give those USDA agents some machine guns, and things get a lot more interesting....