I use CD cases to store my bottle caps. I rip out the black CD tray, leaving the clear, plastic case. One empty container fits 18 used bottle caps in a hexagonal pattern, and 14 unused bottle caps.

The stack of CD cases pictured below holds 300 bottle caps.

As for organization, I have the bottle caps arranged chronologically according to when I got each one. This isn't ideal, which is the main reason why I created the Bottle Cap-O-Rama web site, so I can search by name or visually determine if I already have a particular bottle cap. The case number appears beneath each bottle cap (U001 for example).