I separate mine into categories that are as close to being mutually exclusive and jointly exhaustive as possible first.
For example, I have groups for DVD movies, DVD TV show series, other DVD videos, Audio CD’s, software CD/DVD’s (except games), game CD/DVD’s. I also separate each of those categories into burned discs and original discs
For my original discs, I like to keep the original cases, even if they take up more room. So, I have a tower for my original DVD videos and audio CD’s. I try to keep these in alphabetical order by title on the shelf, so I can easily find the one I want
I put most of my burned discs in disc wallets separated by category in alphabetical order too.