The only way you can launch an external application is via the EXEC FSCommand but that will only work in the standalone Flash player and you can only open applications that exist in a special sandbox folder called "fscommand". Check out this post (http://www.northcode.com/blog/Conquering-FSCommand-EXEC) from my blog for a brief history and some possible solutions to get around the limitations of EXEC.
When your swf2exe tool just HAS to work
there's only one choice... SWF Studio
If you want to run something outside the FSCommand folder you can use my proxy tool, explained in my post. You can also search for proxy in the Standalone & Applications forum here and find a LOT of posts about it (people have been using it for years).
Unless you have a tool like Proxy or a third party SWF2EXE tool, you can't launch EXE files from Flash.
When your swf2exe tool just HAS to work
there's only one choice... SWF Studio
No. JavaScript would have to be executed by the browser. And even if you could use JavaScript or open a URL from Flash running in a browser, browser security would prevent you from launching the EXE.
The Standalone & Applications section of the board here was concerned with this very topic for a lot of years. I've been answering different versions of this same question there since 2002.
If you want a single EXE file that can launch an application you will have to use a SWF2EXE tool.
There are some free SWF2EXE tools that might work, you'll have to try them to find out which ones have the functionality you need. There are also commercial tools that will definitely work, although most of them are dead and gone now.
When your swf2exe tool just HAS to work
there's only one choice... SWF Studio