Typically one would not cite perl, but might cite any packages which perform work relevant to your field. For instance, (since your nick is BioNrd) you might cite a module in the biology (Bio) namespace, but would not cite something like File::Slurp. Citing style will depend on your field a bit, but you might do something like:

[Bio::Foo]
    Bob Smiley, Bio::Foo, Version 2.4.1; 2008. (http://search.cpan.org
+/)
[download]

Update: Yes, R is something else that would often be cited. Loosely, one can think of perl as a general encyclopedia (not cited) but R and Bio::Foo are specialized sources (cited).