Hm, I generally refer to a single .pl file as a perl "script", dozens (or hundreds) of these "scripts" together comprise an "application" or a "program". Of course you also have lots of packages and classes in there, but I've found that if I need to make these distinctions, I'm generally talking to a perl developer anyway, and all these trivialities are irrelevant by default. Just seems intuitive, I suppose I'm just used to it.
Generally I don't care, the only thing that does irk me is saying that, for example, ASP somehow supercedes perl (or Perl); A little like saying that "UNIX was the operating system people used before Microsoft invented the GUI" :)