How do you order the Pokemon in your boxes?

Diamond: I ordered the Pokemon by level naming each box 'Pokemon1', 'Pokemon2' etc.
I also had a box for Unown, a box for useful Pokemon, a box for Eggs, a box for Starters and a box of spare Pokemon for Trades.

Heart Gold: I retained the same system except with a separate box for Legendary Pokemon and a box for Shinies with the advent of the first Shiny Pokemon I actually caught: Caterpie.

Emerald and Leaf Green: I got these for my birthday 6 years after they were released.
I used the same system as my Gen4 games except I named the boxes after the level of the Pokemon inside them e.g. '1-20'.
I also placed fully evolved Pokemon at the bottom of the box and Pokemon that needed evolving at the top (still ordered by level respectively).
Naturally I had a box for Pokemon I was going to transfer named after the game I was to transfer them to.

White: My most advanced and thought out box system.

My main boxes have default names but are ordered by the national dex number of the final evolution. I had to create an spreadsheet to work out where each Pokemon would sit in each box.
I have 2 boxes for Legendaries. A box with a Synchronize Munna of each Nature named 'Munna'.
I have boxes named after a method of Evolution i.e. 'LevelEVO', 'HappyEVO', 'StoneEVO' etc. with Pokemon to evolve by that method inside.
I have a box named 'Special' for Pokemon that belong to certain Teams or are useful in some way.
Once I evolve enough Pokemon and therefore have sufficient space I will remove some of my EVO boxes to make way for an Unown box and some more 'Special' boxes.

So what about you? Do you have some sort of elaborate box system or do you just drop them anywhere?

Soul Silver: Sorted Pokemon by type with 2 Box for Competitively Viable Pokemon, 2 for Spare Legends and Events and 2 for Junk/Fodder Pokemon.

White (Subject to Change): 4 Boxes for Competitively Viable Pokemon, 1 Box for "The Catching Squad" (Lv.100 Gallade with False Swipe, Hypnosis and Mean Look and 20 Synchronise Munnas of every nature), 1 Box for Job Pokemon (E.g. Pickup, Frisk, Compoundeyes Pokemon), 2 Boxes for Spare Legends/Events and 3 Boxes per Region for the other Pokemon (Kanto, Johto, Hoenn, Sinnoh, Unova)

my box system is a joke in my white. I got less than one box full and the top is the pokes I don't like a lot and the bottom are the pokes that I do like . but some of your guys systems sound good I might copy one.

Starters - Herpaderp - Average1 - Average2 - Uncommon - Rare - Legendary - SHINYYY<3

Type. I don't actually catch that many Pokémon if I don't have any intentions to use them so I can mostly get away with grouping types together in ways that might or might not make sense (Fire & Poison is the weirdest combination but I use it every game). Normal and Water get the most and I end up needing second boxes for them. Then I use the rest for my trained 'mons, my HM slaves and Dittos, stuff I don't want to lose track of.

Then I have a box full of Level 1 Modest and Adamant Poliwags who know Refresh. All the older brothers and sisters of the blue Politoed I eventually got for all that. They jealous

I have a Box for each type, but some I combine, such as Rock/Ground and Dark/Ghost, to save space. Then I have a Legendaries box, an Eggs box, an Unown box, and a box for my favorite Pokemon, labeled "My Team". I haven't gotten around to doing this in White yet though, so it's still a jumbled mess.

I also mostly sort my pokemon by types, grouping some (pretty similar to TwistedTurtwig's system). I always have a "Main" box (box #1) where I keep the ones I use or am working on evolving and need to switch back & forth - also I try to make sure I am in "Main" before I close the PC so that all new captures go in there so I can easily find them. Then I also have a box for "trades" and one for "specials" (specials includes shinies and legendaries if I'm not actively using them). Using this system allows me to more easily find one if I need to. I've used this system since I first started on FR a couple of years ago.

i have:
two boxes for pokemon that have at least one maxed IV for future breeding projects
one box where I store my main team, fancy RNG'd pokemon that I received from people and near-flawless breeds of my own.
one for DW females (soon to be two, because my entree forest is getting crowded)
one for my breeding parents
one for shinies and events

the rest are for storing stuff that will eventually be released.

I order mine based on there uses in battle, since I'm a competative trainer. I have a box for legendaries, box for things I'm never going to use, things I want to train later, EV'd things, things I need to breed, things I have in handy for trades (like 50 lv 100 Reshiram/Zekroms for the GTS), and so on. I have about 3 or 4 boxes for each category. I used to do it by type, but then it was too confusing when it came to dual types where I put it.

Basicly I have 1 box for all my important pokes, and all the other boxes for random pokes I catch

On my prized Firered I have one box for all my important pokes, like my main team, legit shinies, a Lv 100 Blaziken I got while doing a solo run on Ruby, an adamant Groudon, and other random ones. And for my other boxes, believe it or not, I have all 386 pokemon in all the boxes (yep even things like Jirachi and Mew and etc, but apparently I lost Tropius somehow but I can get him back easily)

For my markings, I have one mark if its a pokemon I'm about to EV train, two marks if I AM EV training it, and every mark if it is fully trained and on my team

My boxes are as follows:
Boring- Just plain old pokés.
Boring 2- The first one filled up.
Coolio- Pokés that are above lv. 40.
Spesus- Rare pokés.
Legends- legendary pokés.
SupaBox- Where I keep my competitive team.
Box 14- This is full of gibles, I've been breeding for a good one.
Shinybin- Where I keep my shinies, all five of them.
Trios- legendary trios.
Starters- Starters.
Dragons- Dragon types
Hoenn- Another "boring" box, but for pokés that I migrated from Sapphire.
Tom- Pokés that my friend used when I lent him my Sapphire, if he ever gets a ds I'll trade them over.
Box 18- Where I put pokés when I can't be bothered to find the apropriate box.

I thinks that's it, if I remember more I'll add them.

in Ruby, I did it by type, having a box for each type, and some boxes occasionally had 2 or 3 types assigned to them. I later made it by how common they were, from Abundant to Legendary (zigzagoon in abundant, etc.)
In Platinum, I went by types sometimes, with a box for starters, a box for legendaries, and a box for teams, unown, and HM slaves.
In HG, I sorted them by region (Kanto 1, Kanto 2, Kanto 3, etc.), because this is where I transferred them all to. 2 seperate boxes for legendaries (I hunt them hard core ), 2 boxes for starters, and a seperate box for my main team, unown, and HM slaves.
In White, -sigh- I only have 3 gym badges, barely any pokes, so no organization, just half of a box of randoms.