The usual mantra is:

• "Perl" with the capital is the language itself
• "perl" all lower case is the implementation and/or the executable
• "PERL" is just wrong and marks you as a nekulturny philistine

As for how to cite I'll leave to more academically inclined, but I'd probably guess you'd do it similar to however you'd reference any other online-only resource (e.g. the same way you'd refer to Wolfram's Mathworld or Wikipedia in general).

Update: Actually now that I think of it it'd probably be more properly cited however one would cite (if you'd even cite) something like Mathematica or Excel. I was thinking more citing Perlmonks in my suggestion above, not Perl per se.

nekulturny philistine

What the heck is that? :p

An uncultured boor, in as much as using the all-caps form tends to be a fairly reliable indicator on lack-of-plugged-into-the-community-ness. See PERL as shibboleth and the Perl community for similar thoughts and discussion.

The cake is a lie.
The cake is a lie.
The cake is a lie.

When you say cite, do you mean as in a citation on a bibliography / works cited section? I've never done this. For the few academic projects where I've utilized programs (aside from undergrad CS work where writing a program WAS the assignment) I have simply stated in the work something such as 'A Perl program was created to determine blah blah blah . . .'

I suppose you could include a copy of the source as an appendix. I've never done so and haven't ever received negative feedback for that, or failing to included some sort of reference in a works cited section. But to be candid, I'm not confident that I've completed enough of such projects to know for sure if I've done everything right.

Hmm, now that I'm reviewing your post and what I just wrote I realize that I automatically assumed you meant an academic manuscript (like a thesis or whatnot), despite other possibilities. Is this academic? What's proper as far as providing a citation might vary by domain.

Thanks for this and all replies. I much appriciate the input.

You are correct in that it is an academic manuscript. I am in the mode that all software packages/programs (e.g. R: A Language and Environment for Statistical Computing. R Development Core Team. 2008...or SAS. SAS institute inc. 2008...) must be cited.

So, as I said I have not dealt with this issue before, and I wanted to ask those who are more in the know/may have dealt with this before. So again I appreciate the input!

Keep your fingers crossed that the manuscript is accepted! It would not be where it is (or really anywhere for that matter) without all the help I have received here! I am eternally grateful for all the wisdom imparted to a beginner.
-Bio

---- Even a blind squirrel finds a nut sometimes.

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).

1. Cite Programming Perl. The advantage is that it's a book, so you can include authors, publisher, dates, ISBN, etc and, if necessary, point to page numbers. It also has Larry Wall as one of the authors, and its text is highly regarded. The disadvantage is that it describes perl 5.6 and that's likely not the version you worked with.
2. Cite the URL of the source tarball. This is the most accurate, assuming you didn't use a Perl that was modified by your vendor. It does have all the disadvantages of URL citing though: it's non-traditional, the resource may go disappear, or worse, the URL may point to something else than it did at the moment you wrote the citation.
3. Cite the p5p mailing list (and/or its archive). Very unorthodox, but that is the (public) place where perl5 development happens.
4. Cite it as: "Larry Wall", [pumking of the version you used], et al.: "The Perl Programming Language, version XXX", [year of its release]. Possibly with a URL to the tarball.

One other option -- cite something announcing / reviewing the particular release. If you have to, even cite the perldelta for the version. I would assume the author for the perldelta would be the pumking for the release.

Update: And another random thought (and why I mentioned citing a reference, rather than directly) -- there's been an issue in scientific fields regarding how to cite the actual data used in the research, and I saw a talk last week at CODATA by Sünje Dallmeier-Tiessen, where she discussed an journal for the publication of earth science data. They have a standard template for presenting important aspects of the data (where to get it, provenance, coverage, etc.), and have a peer-review process ... so that people can cite the article describing the data set, and standard bibliographic tracking will pick up the relationship.

I have no idea how often it's necessary to cite programing languages, but if it happens often enough, it might be worth people working together to create a similar journal for people to announce major updates to programming languages.

Recently I bumped into the same issue and asked in Chatterbox. It turns out that, at least if you use the BioPerl modules, there are a few peer-reviewed articles that cover the module. In their Wiki page they explicitly tell which articles should be cited whenever the BioPerl modules are used in published scientific articles.