Mine are stacked all over my room. I rip them then put them on a stack somewhere. Not at all helpful in the organization way. I do keep all my DVDs alphabetical, but I only have ~130, so thats easy to do. I store them vertical on shelves that are a few inches taller then the cases.
One thought I just had was to make sections of correspond to a letter, and just alphabetize by the first letter. My local used CD store keeps the majority of their cds sorted by genre and then first letter of the band.
A guy I worked with put them all into cd binders, and he had 10 mostly full 200 cd cases.
He put A-C in the first one, D-F in the next and so on. He left every 5th page or so blank as room to grow on. Worked well for him.
He was a good guy to ask if a customer knew what they wanted but couldn't explain it in a way for me to find it.
Wetzel