Physical media can be hard to keep track of, especially if you're in an environment where you have several people who might be carrying the media around to various locations (or worse, where you have to loan your media out to end users. Don't laugh, it's a fact of life in academia). I've always kept physical media in a file cabinet, using a different hanging file for each package. ISOs were copied to a server in case I ever needed to make a new version, although most applications were installed via rdist (Linux) or SCCM (Windows).
For OS media, I generally threw the minimum necessary for booting onto a thumb drive that I kept around my neck and did the rest of the installation from http-based media.