I have thousands of DVDs neatly filed into storage cases and then placed in RubberMaid storage boxes and finally placed on shelves in my basement. One of my major concerns is keeping the DVDs from being exposed to moisture.
For a bit of added protection, Light Impressions Direct sells reusable desiccant canisters.
Put these in storage containers to absorb any moisture and maintain an acceptable level of humidity. Periodically microwave them to remove moisture and reuse. Very cool.