Not only did I have stacks of boxes on my desk, but on my bureau and closets! I took an afternoon to take all the cds out of the boxes and toss the boxes. It was truly heartbreaking, throwing away my beloved collection. Especially my "The Sims Hot Date" box. It was one of the last big boxes I bought. But the clutter needed to go. It was starting to get too be way to much. A person needs to be able to put towels in a linen closet!
After the boxes were gone, I had a huge unstable stack of CDs. I've always hated dealing with stacks of cases, so I knew something had to be done. It was a much easier decision then deciding to get rid of the boxes. The cases had to go. I went to the store and bought a CD case that held a few hundred CDs. As I was putting the CDs away, I realized that serial codes were on the back of the cases. I was going to need those. So I took apart the cases and stuck the paper in with the cds. Remember this, it is important, because without the serial numbers, you won't be able to install the game. Not all games have them, so be sure to check and double check (and triple check if you feel paranoid like I do over my favorite games).
I feel a huge sense of relief having my games organized. I can easily flip through the case and get to the game. No more dodging falling boxes to find the game at the back.
A CD case or wallet is not the only way to go. There are wall racks, cabinets, and CD racks for the floor or desk too. It all depends on how portable you need the collection.
Good luck with the project of cleaning out your CD mess if you decide to do it. Anything that gets rid of clutter, has to be good, right?