Organizations are not all created equal, and some of them do not want you to know this. Another factor to look at when designing an organization is how transparent it is. Some organizations are required by law to have some transparency at least; in the real world, a charity, for example, is required to maintain records that are visible to the public in exchange for its tax-exempt status, and any attempts to hide its financial records can result in that status being pulled. Other organizations, especially those involved in law-enforcement, will hide as many of their records as possible for security purposes; apparently its harder to protect yourself from the bad guys when they know all of your undercover agents.
[Clarification on transparency: An organization that is required to be transparent is not usually required to be fully transparent. That is, although it may be required to show what it does with funds it raises, it is not required to give out information on its employees. Conversely, a more secretive organization is usually required to compile publicly available statistics, including how it spends most of its money, in exchange for its privacy, especially if it is governmentally funded. In short, there are always some secrets, and there is always some information available on any organization.]
From a writing perspective, this gives you options. A transparent organization, especially one that is required to be transparent, has a number of problems. A for-profit competitor can take advantage of its records in order to take over the charity's niche. This also means that the transparent organization has to be aware that anyone can look at how it is spending its funds, or face legal action; this limits what it can do as regards some non-proprietary patents and how it can organize itself. Because it has to let people know what it is doing, it has a major strategic issue. In a dark universe, there is likely to be a lot of creative accounting when it comes to funds and by-laws in order to hide some items from the public, such as a private army.
A secret organization, on the other hand, will always be under attack, leading its members to have a bunker mentality; at the very least they will be suspicious of new people in their lives. Since everyone wants their secrets, and they need to hide those secrets, there will be layers of security even for the most mundane of day-to-day business. Depending on what they are willing to do to get those secrets, the organization may be in serious trouble. You will also need to determine the effects of something like Wikileaks; does the public really need to know the identities of those that are testifying against mob bosses, and if it does, how will that affect how the prosecution deals with cases? There are issues of how well two secret organizations will cooperate on the same case, and to what degree they will share relevant data.
Out of all of the various axes, this one is probably the most interesting to play around with, especially in darker universes. Enjoy!