Perhaps the most obvious way to organize your CD collection is by artist name, alphabetically. For each artist you can either arrange their albums alphabetically, or (my preference) chronologically. Soundtracks and compilations can be placed separately from artists or not, if one prefers. A CD rack with no individual CD slots really helps - no "taking your collection all out when you buy new stuff".

This may seem colossally anal retentive, but it makes it a lot easier to find what you want. Everything does "have its place", but it's not that hard to put something back where it came from. I only own about 75 CD's and I still find it helps.