i sometimes do, but i think over the years i've gotten pretty lazy with it. @[email protected] i think previously, i used to sort them by type, and i sometimes still do, but other times (especially in recent games), i just don't bother at all.
i do miss when i used to sort my PC by type though, because it became easier to find Pokemon that way.
Emerald: First it was by level (see below) but after two years I did it by type, with compatible types sharing boxes (Dragon & Flying, Rock & Ground, Grass & Poiston, etc.).
Platinum, W2, HG, X, AS: By level from lowest to highest. Ties are broken by experience, if it's the same by number of non-status moves, if it's the same by sum of the power of the moves and if it's the same by the sum of the accuracy and if it's the same by the sum of stats. However, I changed some post-Sun to Region of origin, as moving Pokemon was becoming a nightmare.
Sun, Ultra Moon: Region of origin and with no particular order, just one or two boxes per region. I think I'll use the same method for Shield.
I generally don't organize my boxes, but there are a few exceptions where I will:
If I have different forms of a Pokemon, I'll try and keep them together. For example, I like to make boxes for Unown and alphabetize them, since it makes it much easier for me to keep track of which ones I have left to catch. Same with Vivillon forms. I'll probably reserve a box for Alcremie flavors too, once I reach that point.
I also like to keep any teams I have together, so I don't have to look through 10+ boxes for my main squad. I usually reserve the last box in the PC for my main and side teams whenever I deposit them.
Easy: Primary type, with the order of the boxes being the order of the gyms by introduction (with Dark and Fairy switched because I can't be bothered to change the order again), with the Pokémon inside ordered by number. In other words, the order would be:
However, since there were not enough boxes to do this before Gen V, I used the TCG types (minus Dragon and Fairy since they didn't exist), meaning that my boxes were ordered like this:
Given that I've been building a transferable Pokédex for Shield I've had tnem in number order with a box for alt regional forms, a box for Shinies and a box for Gigas...then the Surprise trade/surplus breeding boxes are just a mess!
Normally I don't catch enough mons to make the organisation worth while but I figure this was worth setting up now to save me having to do it once Home is released - thinking my Bank boxes might stay as is until we hear more about when that service gets shut down.
When I was working on a Living Dex in Gens 6 and 7, I kept them in Dex order, but as of Gen 8, I'm only aiming to fill in every Pokédex entry rather than actually keeping a specimen of every stage. So now my boxes are just a scattered mess of whatever I've caught, other than the boxes at the very back that I reserve individually for specific things (my Gigantabox, my Alcremie boxes, Shinies, etc.).
When I am doing a genuine playthrough, I like to set aside pokemon for later in other boxes. Post Game, I like to have teams beside each other, since you have 6 in a line. It would be like, Haxorus and Skarmory in the same row.
And Nuzlockes, I just take pokemon I wanna use later and place them aside
I have a box for legendaries, for shinies, for important Pokemon (Pokemon I really like/my ingame team), and maybe some extras depending on what I have. In SwSh since there are only a few legendaries as of right now I actually put my Eeveelutions into that box so I can keep track of them. In SM I had a box of Pokemon my ex competitively bred for me, and I had a box of Pokemon I wanted to Masuda Method for shinies (which I will make again once I decide what I want to shiny hunt for in SwSh).
I have a few boxes for random Pokemon which I try to go through occasionally so I don't have things I don't want in them, and then I save at least a few boxes for space for breeding.
Currently my last two boxes in SwSh are full of starters and rare Pokemon I will be surprise trading out around the holidays.
I used to do it by type, as I recall, until I started to collect pokémon for the National 'dex in earnest. Then I started to organise by National 'dex number. Then shinies, interesting duplicates, and the like started to disappear into the mass, so I separated those out onto the cart itself, with the majority ending up in the Bank
Until I have more than two boxes filled in my playthrough, I don't care about organizing them. Now, when it goes beyond it then I start with a box for my usable Pkmn and then go by type to the right of it, starting with Grass and then Water, Fire, Electric, Poison and so on. To the left I have a box for Legendaries, shinies and then some for breeding. I usually name my boxes accordingly to the wallpapers that seems to fit the type (for example, "forest", "meadow" and "jungle" for Grass type).
The first box is a temporary box for whatever I catch.
The second box is the main box for my usual team. If I get a shiny, I keep it in the main box even if I don't plan on using it right now.
Sometimes a third box for legendaries.
All other boxes for all Pokémon in the Pokédex order. Sometimes a box for kinds of Unown. Usually by National Pokédex number, but sometimes I tried keeping the cross-generational families together, like the Eevee family
If I'm playing on multiple games (as I did with multiple GBAs years ago), the first game has a useless trade box with common Pokémon for trade between games. The other games are secondary and tend to have messy PCs.
I never organize it during the playthrough, but I organize it after I finished the game and start to complete the Pokédex. I just have to put everything in numerical order and have a living dex because you know.... OCD
In Sapphire, Diamond and White I sorted my PC by having the newer Pokemon in the first 5 or so Boxes while the older Pokemon occupied the other Boxes. But in every other game I don't even sort my Boxes, I just let them get filled with Pokemon that I catch without putting any thought into it.
Early on, I didn't organize them at all (which was really fun when I was looking for something specific). Around Gen III, when it became easier to move between boxes, I did try to be a least a little organized and did it mostly by type with each box further broken down by Pokedex number.
By Gen IV/V I ended up separating each by function. For example, I have a box (or two) dedicated solely to Legendaries, shinies, and Events, another dedicated to teams, another to trading, another to breeding, etc. In Gen V I also dedicated a box I wanted to transfer to Bank/Gen VI. I also name the boxes by what the function is since that is usually what I'm searching through them for.
Currently, in Sword, I'm mostly trying to stay organized from the start since I usually don't end up doing any organizing until much later. As of right now, I have boxes dedicated to:
Evolutions (those that I currently need to evolve. This is sometimes split into "Special Evolutions", such as those that need a stone/item, trade or other circumstance to trade)
To Trade (those I have on hand to trade; includes in-game trades as well)
Breeding (those I want to breed either to get baby/first forms or as breeding projects. Breeding projects get their own species-specific box(es))
Formes (dedicated solely to those with different catchable formes, with the same species being placed next to each other [Alolan Raichu next to Kantonian Raichu, for example]. Species with a lot of formes, like Unown and Alcremie, get their own box(es)).
Legendaries, Shinies, Events, Specials (usually try to keep in Pokedex order, but may split by subgroup.)
Traded/Dynamax (anything I get in a trade or anything caught in a Max Raid Battle. May be split once I fill in the box more)
Teams (Stronger or more often used ones that I'll switch out and use in-game when I need to change my roster)
Other (anything else that doesn't fall into any of the above categories. Not usually organized in any way, though I may go by type or number if I feel like it)
Anything that fits into more than one category will be assigned a box as I see fit. For instance, all Deoxys will likely be placed in the Legendary box rather than the Formes box while an Alolan Raichu that I use on my team will be placed in the Teams box and the Kantonian Raichu stays in the Formes box.