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.