Would every fic on the site be filed under a theme, or just the ones that would fall into the major categories, like Holiday fics and Parodies and etc.?

I'd definitely just do the obvious ones. It would be a real pain to sort all of them, and doing so would end up watering down the results and making many of the categories useless. Plus, most stories are already covered under pre-existing categories anyway (like post-"Gift" or Spike/Xander or whatever).