<p>How can I use command line arguments in a <em>creationComplete</em> event handler? It seems the <em>invoke</em> event happens in my AIR app <strong>after</strong> creationComplete gets called, so I can't use the args in that function, although I really would like to. Any other event that might always fire <strong><em>after</em></strong> the <em>invoke</em> event happens?</p>

I don't think that will be possible. I just checked the sources and the invokes are set up in an enterframe handler AFTER the creationcomplete event has fired. You could perhaps subclass WindowedApplication and try to change that order, but there will probably be a good reason why it is implemented that way.
You can find the WindowedApplication.as file in [FLEX_DIR]\sdks\3.1.0\frameworks\projects\airframework\src\mx\core
Interesting comment on line 2942:
Because of the behavior with the nativeApplication invoke event
we queue events up until windowComplete