Title says it all :P
I'm just interested because I have a lot of trouble deciding how to organise my cards because there are so many.
Originally, I kept them all in one folder, using those poly-pockets that are made up like nine card holders (eighteen if you count front and back together). I had all my Bulbasaur in one slot, then all my Ivysaur, and so on in National Dex order so that one side of one sheet had the first nine Pokémon (the Kanto Starter lines). Used to use front and back, but now I only use one side because of the number of cards in each slot. To clarify further, I only kept one of each card in a slot, no duplicates of one from the same set - they were stored separately.
However, recently, the folder is beginning to burst and so have several of the individual slots due to the number of cards in them. To that end, I've been trying to figure out a way to re-organise them. I'd begun to put them into their sets, so I bought more card pockets and acquired two new folders. To make things even more beneficial, in each slot for the Base Set, I'd store one of the card plus two spares in case they were needed. However, this did not work as, by the time I had more-or-less done all the sets, I could not find the cards I wanted when I wanted them.
So, using the same one card plus two spares system, I have begun to organise them into a modified National Dex order (everything the same, but with Pichu moved so that it is with Pikachu for sake of deck making made easy). What I'm doing currently is having in the first slot of the nine card pocket is my Base Bulbasaur, then in the next slot the next Bulbasaur that I have that came after that in terms of release. So by the time I'm finished, the first pocket has four Bulbasaur and five Ivysaur. I leave the other side of the sheet empty so that if I get any other Bulbasaur or Ivysaur along the way, then I'm not moving everything, just the ones in that sheet and, once that sheet is filled, I'll just pull in a new empty one and carry on the process. I have filled three folders and I've only done up to Celebi. I've run out of folder space and pockets to use XD
I've attached some images of the way I currently organise my cards to aid the explanation.
So, yeah, that's how I do it.
What I wanna know is what people think of my system and I wanna know your systems - maybe people can learn from other people in terms of how best to organise them.