I'm looking for a way to organize and store my note cards so that I can refer back to them quickly. I'm looking for ideas and maybe ways of classifying them, too.

I use note cards when I'm reading, when I hear something profound, or a quote from a great speech. I've found this tactic to be very helpful, with the memory recall issues associated with ADD. They're also easy to carry around. :)

A few questions:

1) Do you use index cards, or are you taking notes on random scraps of paper? (Are they all the same size/east to stack?)

2) Do you prefer having a physical card, or would you be willing/interested in looking at electronic options (either native electronic options, or scanning/photographing the cards)?

3) When you use the cards for reading, is it similar to how you use them in other contexts -- to collect ideas and turns of phrase that you might want to remember and pull out for a speech or comment? Or do you take notes in some other way/for other reasons?

4) What are the difficulties you're having with the current "system" -- are you losing cards, or just can't find the ones you need, or...?

If they are index cards i am thinking: some kind of a flat, soft case ( even if thats not its intended use- look at a cosmetics case even, they have stuff thats not girly :)
Get some post it dividers or tabs
Also colored index cards?

1) Do you use index cards, or are you taking notes on random scraps of paper? (Are they all the same size/east to stack?)
I use index cards. They are all the same size, and I think that size is 3 x 5.
2) Do you prefer having a physical card, or would you be willing/interested in looking at electronic options (either native electronic options, or scanning/photographing the cards)?
I struggle with this a lot. I have a few inspirational quotes on cards that I've taken a picture of and kept on my iPad. The rest of my cards are just on paper with either a paper clip or rubber band holding them together.
3) When you use the cards for reading, is it similar to how you use them in other contexts -- to collect ideas and turns of phrase that you might want to remember and pull out for a speech or comment? Or do you take notes in some other way/for other reasons?
I'm not sure. Let me think on this and get back to you. :)
4) What are the difficulties you're having with the current "system" -- are you losing cards, or just can't find the ones you need, or...?
Having a proper place for them where they are secure and put away. Right now, I have several piles or groups peppered throughout the house, and this drives me nuts. I'd love to have one place for everything, but I don't know what that place looks like. I want to be able to access it in a quick way. I'm thinking of a box for index cards, but that's way too small.

If you have just four or five categories you could use one of those hanging wall thingies. I've got no idea what they are called. They've got 4 or 5 pouches to out things like newspapers into them and they hang from the wall so would be very accessible.

Otherwise like Stef said something like a toiletries or cosmetic bag. They often have quite a few compartments.

You get box folders for loose paper.

I guess a stationary shop would have some kind of organiser or organising folder that you could use.

Index cards come spiral bound.

I use my handy old school metal index card filing box