Underdog category would be interesting. I'm going to assume you mean the sense of Least Likely To Be Popular and not in the sense of Least Qualitative, though the latter would be amusing.
In my head, an underdog would be anything that didn't have elements of the classically popular, so if you could figure out what those elements were on Smack Jeeves, you could apply the opposite. I would say Boy Love, Manga and Sprite comics would be, if not all popular, then at least the most common genre elements...not just in number of comic titles but in interest of readers. Fancomics too have a built-in audience potential based solely on the popularity of the franchise, which makes them less underdoggish.
There are a lot of oddities to the SJ community too that don't really apply to webcomics in general. Normally strips are the more popular format in webcomics, but SJ seems to favour story comics, so I'm not sure what to say about that. Colour comics have it over black and white in terms of popularity, but that also doesn't seem to be the case here. I don't know if that has anything to do with the subject, but there it is.
Like you suggested too, whether the creator has a big following would be good to consider, though hard to police...I'm thinking of folks with big dA or other off-site group followings. Still, it should bear consideration. Then, too, you can eliminate any comics that are already popular, be it among SJ members or off-site.
Of course, the term "underdog" is subjective, so there couldn't be any hard and fast rules, just the informed discretion of the judges. But then, everything else is too, more or less, so it doesn't matter.
So I would say the variables of a "Best Underdog" SJ comic would be anything that was non-BL, original concept, Western/Euro style art or photo comics made by unknown or emerging (maybe the word is novice?) creators.
It might be easier in terms of definition, to go with a category more like Most Underrated or something, though the back of my head seems to recall a similar category last year.
Or you could just do one for the best comic about Underdog. Oo wa-oo wa-oo wa-oo
Those are my thoughts. Don't know if they help or if they're anything that hasn't been considered already.