There are disk tracking utilities out there that you can use to keep track of the info on your CD's, zips, etc.
i use DiskTracker, which takes seconds to catalogue a CD- www .disktracker.com
There are others. More for OS 9 and below than for X, I think. It is crucial to know what CD has what on it without having to insert each and every one! Number your CD's, too.
As for a filing system, I use labels (where did labels go in OS X -- oh my; chagrin) and custom icons (there are utilities that change these easily) to create both visual windows and a coherent hierarchy. Go for hierarchy over visuals -- keep your naming conventions straight for all jobs, i.e. chose pictures, pics, images or Photos -- stick with one and don't change it.
Try and name your files in a manner relevant to the folder structure it is in so that you have some idea of where it might go if it gets moved (or so you can spot out of place items).
Use aliases!
I use Toast to burn CDs. Burn ISO 9660 disks. Select resolve aliases so that aliases point to files on the CD instead of on your Hard Drive. ISO 9660 allows you to reimport sessions if you need to add or remove (!) later on. You are basically overruling the disk directory, so you can add new files, remove (it only hides) them, reorganize and rename previously burned files and burn a new session that doesn't result in an extra volume being mounted or the reburning of all the files already ON the disk.