You can launch command line tools (including the perl interpreter or 
any other command) via AppleScript using "do shell script". Apple has 
a good technote on its use and capabilities here:

http://developer.apple.com/technotes/tn2002/tn2065.html

Regarding the best implementation: Behaviours are not just for 
controlling applications. Instead they were named that way because the 
remote will have a different behaviour depending on which Behaviour is 
currently active. Examples for Behaviours that are not responsible for 
a specific application include the Audio & CD/DVD, Virtual Keyboard, 
Virtual Mouse, Virtual Remote, ... etc. Behaviours.

Behaviours act as the parent of a number of Actions (which themselves 
consist of Actors, which can be keyboard or mouse wheel events, 
AppleScripts, etc.). Or, as their "container".

What you'd likely want to do is create an action that uses AppleScript 
to execute the shell command of your choice. And then have that action 
to be globally available (by checking the respective checkbox), so it 
can be used as a menu item as well as being mappable to the button of 
a remote.

You can either just mark an action global in the Behaviour 
Construction Kit (it'll then turn up in the "Miscellaneous"-group in 
the Mapping and Menu prefs). Or you can also create a Behaviour to 
contain that action.

You'll find more info and step-by-step instructions in the Remote 
Buddy Help (under "How do I ..") as well as in the video found in the 
"For Developers" subpage of the RB site.

Best regards, 
Felix Schwarz