the 1st gen cl pocket is also too shallow for CD's... thats the one I have. I just put pens and other "things" in there, hehe, I even wired an electromagnet lock that locks the lid from a switch, so if my car gets searched I can place things in there I dont want cops to see.

Your best bet is to use an open pocket and let the cd's hang out a little... all the pockets you'll find wont be deep enough because they wont fit due to the placement of the radio bracket.