I'm currently using CD cases to store my bottle caps. I rip out the black CD tray, leaving the clear, plastic case. One empty container fits 18 bottle caps in a hexagonal pattern.

By using CD cases, I can store my collection in racks or shelves meant for displaying and storing CDs. So I can forsee having several hundred bottle caps stored in a compact manner. 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. Admittedly this is not ideal, which is the main reason why I created the Bottle Cap-O-Rama web site. On the internet, I have my bottle cap images in a database which can be searched by title and beverage type. In the future I can add metadata in terms of date, where bought, and eventually the country of origin. This amount of cross-indexed information would be very hard to do with the physical bottle caps.