I've got a lot more than 3000 cds and cdr, plus another couple of thousand dvds. Living in a small Tokyo apartment I finally had to take radical action, as I literally ran out of space to store the stuff.
My solution was simple, I dumped all the jewel cases and dvd boxes, put everything in paper covers,inserted into the cd booklets, made an Excel a-z list and put everything into storage boxes which are kept under the bed, on top of wardrobes and any other space available.
It's not an elegant solution, and one that would probably not be acceptable to anyone living in a bigger place, but I does work quite well.