Ultimately, I think your Penny Arcade example shows that you are 1. thinking about how to properly cite sources with regard to how people use the internet and 2. providing a level of verfication/proof to people who might be reading your thesis. I think this is the important thing: That you are trying to properly cite them and you’re being transparent about it.

Actually, I’m citing the creators of Penny Arcade as “Krahulik & Holkins” because those are the only names printed on the comic itself, or even the page where the comic appears. See vertically printed text on the right—“©2004 Mike Krahulik and Jerry Holkins”—hence the decision to print the names out of alphabetical order, as well. Admittedly, this does make things confusing when citing their “news posts” elsewhere, which are written under their pseudonyms. Considering that they have widely known real names printed on their other work (under which copyrights are attributed), I have simply used their real names whenever citing them.

Mind you, I have whole other sets of rules for citing things from people who I just happen to meet at cons and then follow up with online, which is more geared toward protecting their anonymity. I think the creators of Penny Arcade (and a handful of other “internet famous” people) constitute special cases with regard to the use of pseudonyms, though.

That said, I’d probably in the works cited page listed Krahulik and Holkins writing as Gabe and Tycho. Or conversely just cite them as Gabe and Tycho with a note that their real names are Krahulik and Holkins.

I’d cite a pseudonym with a first and last name just like the twain article.

It is interesting that you’re (hopefully) happily grabbling with the cutting edge of academic citations. And I’m glad you are grabbling with it.

Seems to be the way to go. You’d cite “Twain” and not “Clemens,” e.g.