This is a somewhat old topic born with the original FLfile library by Guy Watson: the undocumented runCommandLine JSFL command, which still exists in FLfile. Previously we had FLappleScript, but it stopped working some time before runCommandLine was available for us in the Mac (IIRC).
FLfile.runCommandLine("echo 'ok' > /tmp/sample.txt;open /tmp/sample.txt"); // works in Mac, use your windows' shell knowledge if you use Win
Or this one:
FLfile.runCommandLine("osascript -e 'tell app \"iTunes\" to playpause'");
These are stupid examples, but I have a couple of interesting projects using a mix of various technologies, including JSFL and Flash, AppleScript, the shell and Illustrator, etc., which is a very promiscuous mode of scripting, but very funny and inedited for many people.
This command only returns (I think) the exit status (1 or 0), but still there is a bunch of ways to get your data (such as writing it to tmp files and reading them from JSFL using FLfile.read())