What a great idea! I have a ton of jewel cases stuffed in my closet too. As soon as I find a good glue, I'm going to work!
Edit: Yay, I found plastic glue in my basement! I made a mini one, as I have a very small bought CD collection (most of my CDs are burnt, and in those portable CD holders. I used the thinner jewel cases glued together, the kind that you buy blank CDs in, because I didn't have enough thicker ones. I also had to put a little mini support in the middle because the top shelf kept leaning, guess the glue wasn't quiiite strong enough. But ah well. Thanks for the awesome idea! Here's a picture of my version:
Unfortunately I forgot that I should put the decorating inserts in beFORE gluing the whole thing together, but I managed to slip some blue CDs in the top, so that's fine with me.