I have terrible but defined habits for my ROMs. I use the same folder structure for all of them.
./[platform]/[game]/[game].zip
./[platform]/[game]/[game].iso
./[platform]/[game]/saves/...
If it's a series, using Pokémon as an example, I also have:
./Pokemon/Backups/[game].zip
./Pokemon/[generation]/[game]/[game].iso
So it's not that good of a backup, mainly there in case the iso corrupts, but I think it's better than nothing.
I spent the last 6 months working on a feature. Found out 2 weeks before release that it was being postponed.