I keep mine in loose leaf notebooks meant for cds. Each book holds about 100. I leave empty pockets every 3 o4 4 so adding new ones takes relatively little rearranging. The cds are always easy to find, I keep information, album covers, etc. on the back side of each pocket. The whole collection takes a lot less space than they did in even the slimmest jewel case/pocket and it easy to pick up a book or two to take along in the car.
Although I usually burn copies if I want to have them in my car so that I don't risk damaging the original there are times I want to take a lot of them with me.