Newbies 1-3 - First three boxes where newly caught Pokémon go before sorting.
Favourites - Favourites/team Pokémon.
Warriors - For competitive Pokémon.
Cuties - For cute Pokémon.
Fodder - For random/rubbish Pokémon that I don't intend to use.
Breeders - Pokémon that will be used for breeding (egg moves etc).
Fillers - Pokémon that need evolving/breeding for Pokédex completion.
Relics - Final box Pokémon traded over from previous games or rare/event legendaries go for safe keeping.
And that usually takes up all my boxes with some sections having more than one box dedicated to them. And yes, I did put too much thought into organising them. :D