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.