I spent quite a while trying to figure out how to launch a second Automator workflow based on a conditional in perl, and this was the best I could come up with. Basically, I set up my conditional in perl (as part of the initial Automator workflow, in the Run Shell Script action), and if that condition was true, it executed this command:
system ("open /Users/myuser/Desktop/sendit.app");
(sendit.app is my second "branch" Automator workflow application.) It's pretty obvious in the end, so it may not be much of a tip, but I couldn't find how to do this anywhere I was looking.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20080420182839338