When working with Flash from a webpage or as a desktop app, you are limited to a small security sandbox and you will not be able to make any relevant OS call. I thought that switching to AIR would give the developper more flexibility but it doesn't seem correct either. From "The Pros and Cons of Adobe Air":
  AIR apps have
  file access, clipboard access, support
  multiple windows, support drag and
  drop, and can trigger notifications
  (toast in Windows). If you app needs
  to interact with the desktop in other
  ways, the chances are that AIR is not
  suitable. For example, there is no
  access to COM automation, and no way
  to execute external applications. The
  reason is to maintain cross-platform
  compatibility. That's a worthy goal,
  but it would be good to have a way out
  of the sandbox. Unlike Java or .NET,
  you cannot extend AIR with custom
  native code libraries. Nor can you
  call operating system APIs.
As Alex Jillard commented, if your swf is called inside a C# desktop application, you should be able to access more OS funcionalities although I'm not sure how.