I have way too many CD's (about 2200, actually). Years ago, I discovered the best way to store them all was in the Roladisc system developed by CD Projects.
As you can see, the system involves removing the CDs from their jewel cases and filing them in sleeves in a rolodex.
This system has worked well for me. However, all my rails are full and CD Projects doesn't make this system any more. I've been hunting around the Internet to see if anyone still carries them. SO far, no luck. I plan to keep trying. It's a bummer when someone makes a product that you like, and then you can't get it any more.