If you have a lot of small, unused cables such as computer cables, audio cables, or video cables, you can coil them and store them in a CD spindle. This will keep them neatly organized and out of the way, and since spindle cases are usually transparent or translucent, you can easily see which cables are inside. You can even place unneeded CDs in between each cable or type of cable in order to keep them separate.
You can use a CD spindle to hold small paper towels or toilet paper. This is particularly useful for outdoor excursions such as camping and picnics. If the paper towels aren't the right size for the spindle, you can simply cut them with a serrated blade or electric knife.
You can drill a few small holes in the bottom of a CD spindle, then use nails or small screws to mount it on a wall with the plastic cylinder sticking out horizontally. This will allow you to hang headphones or cables from it for quick access. For an easier but less secure version, you can simply use double-sided duct tape to mount the spindle to the wall.
It may go without saying but of course you can use a leftover CD spindle to store CDs or DVDs. This uses much less space than disc cases and binders, although it can take a while to find a particular disc.