I don't know how many cards I have, but they must be in the thousands by now...I'm not sure about you guys, but I have never thrown out a Pokémon card. Ever. Even cards from old sets, commons I must have like fifty of, and completely useless cards I keep.
I'm also weird in that I keep them purely by alphabetical order. I really can't keep track of the order of the sets, or who is from what set, for that matter. When I put together a deck, I check the symbol at the bottom to see if I can use it or not. THAT I have memorized. I don't organize them by type either, as when I want to put together a deck, I think of a specific Pokémon (say, Empoleon) and work from there. This is how I arrange them:
1. Pokémon come first. Then Trainers/Supporters/Stadiums. Then Energy.
2. Within each of those three major categories, they're put in alphabetical order by name. Pokémon are always organized by species name only, which means, say, Misty's Tentacool is organized as "Tentacool."
3. Within a single species of Pokémon, Pokémon whose card name is simply the Pokémon's name are always first, followed by Pokémon-ex, then Pokémon Level X, then Pokémon-*, then Dark Pokémon, then Light Pokémon, then Owner's Pokémon in alphabetical order of the owners' names. I don't count the phrase "Deta Species" as part of the name for organization. I don't think there's any species of Pokémon with every variation of that yet, however.
4. Pokémon with multiple variations of itself and have different names (such as Wormadam) are organized under the name of the Pokémon, then the forms they have in alphabetical order.
5. Pokémon of the same species and the same prefix, suffix, or lack thereof are organized by set in order of release (I keep a list), then POP sets, then Trainer Kits, then Promos. For organization, rereleases, such as those in Power Keepers, count as sets of their own. This also goes for Trainers, but not Basic Energy (as they always seem to get mixed up no matter what).
6. Pokémon of the same species, card name, and set are arranged by collector's number from lowest to highest. Promo cards with the same name are arranged in order of when they were released, and if released at the same time, by the number in the corner.
As for what I keep them in, as I always keep them in sleeves, I put them into boxes. I used to use rubber bands to hold the blocks together, but I found out that they damaged the sleeves over time, so now I just use pieces of cut cardboard as dividers. I began with a box of Teddy Grahams (unintentionally giving me the nickname "Teddy Graham" for a short while), then moved to a small plastic pencil box. When that overflowed, I put the rest into a lunch box. Each time the last box would run out of space, I would find another box to put the rest of them in. Currently...
The blue pencil box holds Abra to Bellossom.
The blue lunch box holds Bellsprout to Dragonite.
The green box (which I believe originally held chocolates) holds Dratini to Mareep.
The brown shoe box (formerly held Dinkles) holds Marill to Shelgon.
The white IKEA box holds Shellder to Zubat, all of the Trainers, and all of the Energy. (It's a huge box.)
The orange-lid shoe box holds the deck I use at the moment, plus game supplies, such as dice and glass drops.
These are just guesstimates, as I don't have my cards with me at the moment.