Gotta arange em all! PC Boxes

I used to kinda do it by region. If memory serves correctly...

I never played DPP, never really got into B/W, and I don't own XY... So these are for HGSS.
Kanto | Kanto | Johto | Johto | Hoenn | Hoenn | In-Game Trades | Pichus (For the two Pichus in HGSS)

Since then, I've redone it by level.

100 | 90-99 | 80-89 | 70-79 | 60-69 | 50-59 | 40-49 | 30-39 | 20-29 | 10-19 | 1-9

I arrange them based on type. Here's what I did in the 3rd gen games:

1. Forest - Grass
2. City - Normal
3. Desert - Psychic
4. Savannah - Ground
5. Crag - Rock/Steel
6. Volcano - Fire
7. Snow - Ice
8. Cave - Dark/Ghost
9. Beach - Fighting
10. Seafloor - Water
11. River - Bug
12. Sky - Dragon/Flying
13. Polka-Dot - Poison
14. Machine - Electric

I rarely ever rearranged my stored Pokémon and boxes. However, I would change to the next empty box when I found that the current box was getting close to full, leaving one or two empty spaces when I switched boxes.

As I am more of a collector, I am either sorting by number, when I make a living Pokédex (Like in Pokémon Y), or making boxes for "Still needs to evolve", "Need egg" and so on

The WORST part of Organizing Boxes is....

WHEN NEW BOXES APPEAR! It just throws everything off!

I got one Box for HM and utility pokemon

Next box is for EV/IV pokemon

Next is WonderTrade

Next is awefull wonder Trade pokes I keep for the Lottery

I also have boxes for foreign pokes, and IV Awesome Dads to D-Knot

I order them by national dex number (1-30, 31-16 extra.)and name each box the number it contains.

I have a lots of random boxes, one legendary box, one shiny box, few boxes for my team Pokemon that I want to train/breed/IV train and one box for event stuffs.

I have special boxes for shinies, my Vivillon collection, and Pokemon that are particularly important to me. Everything else is just dumped into boxes willy-nilly.