I've seen two systems for labeling the innards of machines.

One uses those label machines that let you type out something and then spit out a thin strip of sticky tape (like this) - you can find small, low-capacity ones pretty cheaply on ebay or in the backs of office supply catalogs.

The other system is lower-tech, but may end up being significantly more expensive per machine. It involves a polaroid camera and a sharpie. You take two pictures of the innards of the box, wait the five minutes while the picture develops (remember, unlike the song, Polaroid recommends against shaking the picture to speed development), and then with the sharpie label everything in the picture. One picture is then taped to the outside of the box and the other picture is placed in a hanging file in the sysadmin's office, along with any other necessary paperwork for that machine. In a pinch, you can substitute a quick sketch of the inside of the box for the polaroid - again, copies go both to the file cabinet and on the outside of the box.

With both methods, you need to be certain to keep the basic materials in the machine room so that they are there when you need them: have a designated spot in the machine where the label maker or polaroid camera (and possibly pad of blank paper and pen) belongs, and always return them there after use. (label makers are especially prone to wandering about and not being findable when needed if this is not enforced)

I suppose that masking tape and a sharpie would also be sufficient for some labeling purposes.