Weird... For the stuff I actually own I have 2 5 foot tall spinning towers which can hold 200 plus CD's. All my music has been converted to MP3's and stored on about 60 CD's which I keep in a CD folder. This is done for convenience and to save on wear and tear.
PSX and Dreamcast games get the deluxe treatment by keeping them in the original cases and on some type of CD based holder. Whether it be a rack or a smaller spinning CD holder.
My most used Non originals (backups

) get stored in folders for easy access. All the rest usually goes on those CD spindles that most CD writables come on these days.
A few special items (like emu related stuff) go into folders for easy access.
All games using DVD style cases (gamecube, ps2, xbox) stay in their original case.
I think that about covers all CD related material and how I store it.
I just really need to find a better place for my music CD's cause for the most part I dont use them since I converted them all to MP3. Maybe I'll just box them all.