Ok so this is how you do that for desktop applications.
-First of all in the application descriptor file set allowBrowserInvocation to true:
true
(http://livedocs.adobe.com/flex/3/html/help.html?content=File_formats_1.html#1043413)
-The application must listen to BrowserInvokeEvent at the start
and then you can use the arguments passed to the application like this:
public function onInvokeEvent(invocation:InvokeEvent):void
{
arguments = invocation.arguments;
currentDir = invocation.currentDirectory;
}
-You can launch an AIR APP only from an SWF. A SWF file in the browser can launch an AIR application by calling the launchApplication() method in the air.swf file loaded from http://airdownload.adobe.com/air/browserapi/air.swf
Once the air.swf file is loaded, the SWF file can call the air.swf file's launchApplication() method, as in the following code:
var appID:String = "com.example.air.myTestApplication";
var pubID:String = "02D88EEED35F84C264A183921344EEA353A629FD.1";
var arguments:Array = ["launchFromBrowser"]; // Optional
airSWF.launchApplication(appID, pubID, arguments);
For more informations
http://livedocs.adobe.com/flex/3/html/help.html?content=app_launch_1.html#1038008
Hope it helps.