Using Adobe AIR, you can capture only the content which is inside AIR application. AIR does not provide a way to take a screen capture directly.
However, you can make use of AIR 2 NativeProcess APIs to invoke another screen capture utility and get the data from there.
I'm actually writing an application that does this; however, it requires Air 2 because of the nativeprocess functionality
On OS X, look at /usr/bin/screencapture It's basically (as of Leopard I think) included with the os and let's you do all sorts of grabs. I actually ended up writing a tiny C# application that replicates the functionality of screencapture for Window users. Then I just run them as a native process from my application.
Really seamless, but you'll have to wait until AIR 2 is released. Otherwise, there's no way to reach outside the application itself