I organise my monsters by type. Within types, I rarely get so crazy as to alphabetise them, since I take out and add too frequently when I'm brainstorming deck ideas. Frequently I'll keep a bunch of deck-idea cards together, too, until I've made a prelim. deck. In pic case, I have Rocket and Gym Leader cards in their own section.
Just today I bought a new card case, infact, since I have way more cards that have needed a case.
Trainers are usually orgnised my what they do.

Alright, I have my 1-151 pokes in a binder separate from Gen II and above. I usually put the card that appeals to me most on top and put the other versions of that Pokémon behind it. My Duplicates, Triplicates, and so on go in that box and my trainers and energies are inside the tin going in separate directions so they don't get mixed. Not all of my trainers and energies are in there though, not enough room, but most are. I'm in need of a better card case though, like Red just got, and once I have that I will be arranging the doubles by types and the energies will be organized as well. I'll probably move the trainer cards around so they are in order of when they were released.

>>282
1-151 in a binder is a neat idea.
Was that tin out during the early TCG years, or was it non-TCG in origin? I just don't recall it. Also, get one of those card cases - it's only 5 dollars.

Also, adding to my organization:
Like Aggron, if I have more than 4 of one copy, extra go in a separate storage-type box. Since you can only use 4 of any one card in a deck.

>>283
I'm curious about that myself because I also have a dark green one with some bug and grass types on it(current position is unknown)and I used to use that one to store some of the small figures, but I can't recall if I originally got them via TCG. To Google I go.

I put my cards in a supermarket fruit box and put the box in my closet.

>>282
This is SO BADASS.

mine in folder by color, both for pokemon and MTG then at the end ill just organize the energy/lands respectively

pretty much the same as my magic cards.

all my lands/energy in separate leftover deck boxes sorted by color

then the beef of the organization is by color/type. in the case of magic they get organized in the box/es*depending on how much of the color i have* by creature, sorcery, instant, enchantment and enchantment aura. Artifacts and multicolored had their own separate boxes and creatures get sorted alphabetically by creature type and within creature type in alphabetical order in the case of pokemon each group of types gets sorted alphabetically

and for Pokemon support cards get sorted on their own by type and in alphabetical order

i feel so weird saying this, but mine are all by set, then within that, by number order.