I've currently got my Megadrive games sorted by box design, and a tiny subsection for Japanese games.

Same thing for Dreamcast, where I've got the Japanese games first, then the PAL ones (alphabetically always).

I put all my old Amiga games (those with the smaller boxes) together, but they're unsorted. Don't have enough room, I just have to fit them in there somehow ;)

As for the CD32, which is the system I've got the most titles for, I used to sort them by colour at first, but now I put them all back into alphabetical order, it's just easier to find something that way. I also printed out stripes of paper with game names for titles that don't have a CD cover, so that I can find them more easily.