Pretty much everything is alphabetical for me. All the US TG-16 stuff is alphabetical.
Japanese PCE on the other hand, I have organised by media (Hucard, CD, SCD, ACD). Within those areas, I tend to group together similar games; fighters, puzzles, shooters, etc.
Works out just fine.
The only except is Bomberman '94. I group that with my other US titles so Bomberman, Bomberman '93, and Bomberman '94 are grouped together.
The games are stored in their jewels cases. Any spine cards I place inside the manual for that game. The exterior boxes for the TG-16 games I store elsewhere, where i have to dig them out.. One day I'll do soemthing more productive with them...
Something a bit unusual I do with my US Turbo Grafx games, is I keep the instruction manuals seperate from the cases, due to over time sliding the manual in and out can cause some of the artwork to smear. I have a CD caddy that the manuals fit in just fine. All the manuals are alphabetized, so it's easy to find what I want.
I'll post some pics later.