Keep your CDs functional and keep them in a CD case. Computer programs stashed in envelopes look safe until you need the discs and discover they've been nicked in the edges or have cracks and scratches. Movies and music are never the same in a damaged disc.
CD cases vary from hard jewel cases that will protect your disc even when sat on or dropped, to fabric and foam car CD cases easily attached to your visor or dash. Even more convenient are book carry cases that zip up, your discs in individual sleeves inside. Saves space and saves you time hunting down that record of your cousin's engagement party.