
I put all the shoes in big plastic bags by size. I reuse plastic bags and they are very useful for shoes even if they have a small hole or two (unlike, say, for chicken broth).

I separate the boy and girl shoes (one big plastic container for the girls, two for boys now that First Son is five and we've collected quite a few).

It's really easy to switch shoes (in with the old and out with the "new"). I keep the empty bags right in the bins so they're ready for the switch. It's also easy to take a quick stock of what we might need for upcoming sizes. Since they're stored by size, it's also very easy to see if we've got redundant shoes and could spare some for someone else.
Check out more organizing posts over at Works for Me Wednesday!