We're working on the next issue of Comixpedia which we slated as the "Short Story Issue." If you have short story webcomics you'd like to bring to the attention of Comixpedia post a comment here.
The whole idea of a short, self-contained story in comic form is pretty straightforward to me. It has a beginning and end which rules out not only unending serialized sagas but also most one-off gag strips which really don't have much of a story to tell. I'm sure we could argue about that latter point but I think it's essentially true.
Which brings me to the WCCA category of OUTSTANDING SHORT FORM COMIC which you might think is intended to recognize short story webcomics. Not true! It's actually intended to "recognize comics with shorter formats with regular gags, or beats to its story to reflect each individual strip. Traditionally these comics fit (but not restricted to) 'Comic Strip' formats."
Two things: one, not having a category to recognize excellence in short, completed webcomics is a big omission. Not only is that a fairly distinct form hard to compare to other more sprawling works, but by definition, such a category would have the benefit of being comprised of completed works. Two, given its definition it's hard to understand what Outstanding Short Form Comic recognizes that Outstanding Comedic Comic does not. Nevertheless if there is a need to recognize "short form" comics as described by the current WCCA category, why not recognize the actual individual instance, i.e., the Perry Bible Fellowship strip for such and such a date. That would help to distinguish Short Form from Comedic Comic and more clearly tie it to its purpose.