Hm....
-Boxes are sorted by levels, in increments of ten.
-My level 100 box, and only that box, is also sorted so that Pokemon of the same species are side by side.
-Nothing in my boxes is allowed to hold an item.
-Double saving sometimes
-All teams, no matter what have at least one Flyer and one surfer
-Always carry 120 Ultra Balls. Don't ask me why, but I always have this many before I go anywhere
-Always carry 50 Revives, Full Restores and Max Potions, along with 100 Max Repels.
-I always have at least one Pokemon with a type advantage over the next gym, and all my Pokemon at least 5-10 levels higher than the leaders.
-One game, currently my Black 2 holds all of my event legends, level 100s, fully EVed Pokemon, and Pokemon with nostalgia value. Any Pokemon of importance are usually moved to this game posthaste once I beat the main story on another game.
-Never leave anything in the Daycare longer than it takes to get an Egg...
That is all I remember offhand....