My cards are organized by language, and then by set. I use letter-sized binders for English and Dutch cards (though I'd like to get an A4 binder for my Dutch cards sometime) and half-sized (4-card per page) binders for my Japanese cards. Currently I have, for my English cards, one binder for BW, one binder for HGSS/CoL, and one binder for pre-HGSS (don't have nearly as many of those). Japanese cards are one binder per 2 sets, except for Dragon Selection which has all cards in the binder because they're all holo and gets a binder to itself. I keep all holos and RHs in the binder, and one of each C/U in the binder as well, with my bulk in large bulk boxes. Ultra/Secret rares get sleeves and toploaders and are in a separate small tote along with sealed product and miscellany (Pikachu dice, Pokémon branded sleeves, coins, etc).
Currently all of it is wrapped very nicely and hanging out in boxes somewhere in the UK, going through customs. :< Except for BC and BW8 which I got after moving, those are hanging out in sleeves, with SR/URs in toploaders, in my cabinet to keep them away from dust until I get my binders so I can sort them properly. It's kind of driving me nuts, all these cards not properly sorted.