-Organize PC pokemon by type, like BOX1 is Normal, 2 is Grass and so on. Then I have other boxes for Eggs/babies, legendaries, traded, transfer, party pokemon...
-All of my party pokemon (like ones a group into a party for online battles and such) need to have a nickname.
-I will not use a pokemon just for an outstanding trait like high defenses, speed, or attack, or a good ability, if I don't like how it looks.
-I must have certain number of items. Like: 15 potions, 25 super potions, 50 hyper potions, 75 max potions, 100 full restores. This applies to status healers and things like soda pop and moomoo milk as well. o.o
-Under no circumstance can 2 pokemon in one party have the same type.
-I generally never switch out party pokemon for the first story playthrough and postgame, after I catch it. So the pidove I caught on route 3, was still with me when I battled Alder (evolved though).
-Eggs are always hatched in one location for a game. For Black and White, its Skyarrow bridge, for most others, its the Cycling Road or Pokemon League.