Hi PoJo,
Here are some tips for organizing cards, and they may be helpful if you
collect/trade/play often. 

First, if you keep a binder, you'll need lots of pages. I recommend the Ultra
Pro card pages. They are a bit more expensive than some others you'll find,
but they're the best ones available. 
If you have a lot of a certain card, don't stick all your doubles in the same
slot. It'll just make your binder heavier when you have 13 Slowpokes crammed
into the same slot. A few of the card in the same slot is OK, but stick to
two at most. Don't put doubles of holos or good rares in the same slot, the
one behind it might get damaged.  If you really have to put 2 of the same
card in the slot (only if it's a common or uncommon usually) you might want
to put the 1st edition version of the card on top to display (if you have
one.)
Another binder suggestion is a price guide. You can probably find some sheet
protectors that fit into binders that can hold a sheet of paper in an office
or stationary store. Print out a reliable price guide and stick it in the
sheet protector. This will help in sales and trades.
In your binder, it's good to keep them in some kind of order.  Some
suggestions are:
Numerical order (by Pokémon)  If you memorized most of the numbers, this is
very convenient. However, when the new expansions come out you'll need to
rotate most of the cards to make room for the Dark Alakazam and Sabrina's
Alakazam next to your Base one. You might want to leave a space, or put a
placeholder, like a common card you don't care about or an energy, and you
can either leave it blank or write the name of the card in permanent marker.
Numerical order (by card number and set)  This is easier than others to set
up, providing you have a card list.
By Type: I don't suggest this one. If you get another card of that type and
you didn't leave a space, you'll have to make some room.
By Rarity:  This won't put them in a specific order but it's easier to flip
to your holos to show off.

If you're missing a card, or if it's already in your deck, put an energy or
something else you can afford to give up and write the name of the card
missing on it.

For your valuable cards, and you want to keep them in perfect condition, buy
some Ultra Pro acid-free top-loaders. Thin card sleeves aren't good by
themselves unless you're using them for decks, so here's a way to keep a card
in great condition:
First, get the card and put it in the thin card sleeve, upside down, and then
put it in a hard plastic top-loader. This way, if something small like sand
somehow gets inside the toploader, it won't be able to damage the card
inside.  A card placed in a toploader alone is prone to small scratchy things
falling inside the toploader and scratching the foil, if you're wondering how
your Charizard straight-out-of-the-pack-and-into-the-case got damaged when
you never took it out.

If you're a player as well as a collector (like me) and you're using a rare
and valuable card in your deck, buy a bunch of thin card sleeves. They cost
about 1¢ each, and you can buy boxes of them cheap. Wizards sells Pokémon
Deck Boxes with 60 sleeves and a plastic box, but these are too expensive
($8-$10!!) and don't come with replacement sleeves if one gets damaged or
lost, but Ultra Pro sells 100 card sleeves in a cardboard box, which is a
good deal (about $5) and makes a nice deck protector.

Well, I hope all of you collectors and players benefit from these tips to
organize your cards and keep them in good condition! Enjoy!

-Will
(raiden9984@aol.com)