So, let's look at organizations in-depth for a moment; specifically, what kind of organizations are there? More to the point, how useful are they from a writer's perspective?
When it comes down to it, there are four ways to grade a potential organization: Pragmatism/Moralism, Sinister/Friendly, Secret/Transparent, and Supportive/Hostile.
Pragmatism/Moralism: This refers more the organization's moral standing relative to the general populace, and to what degree those morals are implemented. A pragmatic organization will tend towards dealing with any situation as expeditious as possible, and cares more about the results than the context. They have no problems using assassination, blackmail, and discrediting a target in order to accomplish their goals. It should be noted that such an organization can have moral reasons for this stance; MI6 is willing to do almost anything in defense of England, for example. New agents' conflicts are usually those involving their conscience (“Would you kill a four-year-old girl in order to save lives?”), whereas older agents are more worried if they still have a conscience; agents of such an organization are going to be world-weary and have some sort of vice that they engage in in order to feel alive. Sort of explains why James Bond has that issue with beautiful women...
A moralistic organization, however, is more interested in maintaining the high ground. The agents are going to tend to be more intelligent than more pragmatic agents, but they are also going to have more hurdles to deal with; after all, they'll need to allow for the various rights of the target, and will generally be seen as softer than more pragmatic agents. This means that they need to more circumspect than pragmatic agents, and will actually use the threat of using a more pragmatic organization to stop bad guys (“Deal with us and you might actually live!”). Also, they are more likely to use devices that have stunning options to slow down targets, and will gather more detailed evidence; the more pragmatic agent would just figure out a reason to shoot. Besides dealing with targets that want to kill them, all agents will have conflicts based on their conscience; besides having to deal with innocent victims, they will have to deal with possibly letting a dangerous criminal go. Suffice to say, some have the same addiction problems as pragmatic agents, just due to stress.
Although the stereotype is to use pragmatic organizations in dark stories and moralistic ones in comedies, they can easily be switched. The major concern you should have is what kind of point you are trying to make. A pragmatic organization is great if you are trying to make a point about people doing whatever they need to do, but can also make the point that sometimes you need to do hinky things in order to preserve things. It can also be used to show what happens when an organization takes itself too seriously.
A moralistic organization can be used to show that everyone has rights, and those rights take precedence over the group. It can also be used to point out that a rights-based enforcement system is ludicrous. Of course, if you just want a really friendly police system, this works as well. However, don't make the mistake that this can be a shallow system; sometimes there are good reasons for why it's been set up, and those reasons are very good.
Of course, you can always go with a middle ground (which is where most organizations seem to be), in which case your organization is basically one that allows rights whenever possible, but isn't afraid to shoot. You can also mix and match, where each agent makes their own decision on how pragmatic they are, or have an organization that has a specific unit that's very pragmatic, but the rest of the organization tends towards moralistic ends.
Next Up: Is your organization user-friendly?