Ground/Rock
Dragon/Dark (I combined the types that had the least amount of pokemon in them to give me more pc boxes to use)
I used to do that on the older games with limited amounts of boxes, but on Y & OR I decided to use one box per type. But like you said, some types end up with only a few in them, and some overflow into several boxes (I'm looking at you, Water-type!). So for Moon, I'll probably recombine the less popular types.
I keep box 1 for the Capture box. I leave that one selected so wild pokemon I capture end up there and are sorted out into type boxes. The boxes after that are all the type boxes.
Then I wrap around to the last box, which is where I keep my current "best team", HM slaves, capturing specialists, etc. The next couple of boxes before that are for breeding projects, a couple of donor Dittos, the Magcargo I use as an incubator , etc.
Then "before" that are three boxes full of Legendaries transferred from earlier games, event pokemon (go go Shiny Eevee from VCG10!), pokemon traded from other trainers and other Lotto fodder. Like somebody else said I hardly ever get less than a PP UP in the Lotto. I've only got one other Master Ball though. Ooh! I forgot to mention that those boxes also have my Kyogre, Groudon & Rayquaza transferred through the generations up from Emerald.
Right now on Pokemon Bank, I've got boxes 1+ dedicated to my Living Pokedex. I'm on 718 right now, just waiting on Diancie, Meliotta and Volcanion to roll around on the Pokemon 20 gravy train. From 100 down, I've got a couple boxes of perfect Eevees with various natures and/or the hidden ability. I'm thinking about putting in some type boxes to store excess "good" pokemans as well.
And speaking of box organization, I've been replaying Yellow quite a bit, and man, the crummy organization options, and the extremely limited item storage is really annoying. I'm working my way through Victory Road and between my backpack and the PC, I've probably got about 6 item spaces open. I had to burn a couple of crap TMs to have room for the good stuff. Who that that Water Gun or Bubble Beam were good for TMs anyway? It would be nice if you could get rid of things like the S.S. Ticket or Lift Key after you're done with them.
I just reminds me of how glad I was to get Pokemon Stadium, when you could actually rearrange and store extra junk and pokemon.