I keep all my HuCards in sportscard binders, 4 per page. One binder for PCE and one for Turbo. I need to get more though, since they're both too thick.
I put all my Turbo Super CDs together and try to arrange them by spine color, followed by Working Designs SCDs.
Same deal with Turbo CD2's, but I put FS & ML first, then the Valis style cases by color, then Working Desings, the PCE style CD2's.
I keep the highest evolved formats higher on a shelf or first in a row.
So ACDs are at the top of my PCE rack, then SCDs, then CD2's, then HuCards.
I arrange PCE games by specialness, mainly by favoriteness. But pricey titles get bumped up so I can keep track of where they are. Questy/RPGs get ranked highest because they're my favorite genre, then actiony/platformy stuff(
since it feels more questy than the rest), then shooters, then games I'd actually play, then the junk like mahjong and sports.
So Drac X, Snatcher and Winds are in the top batch of SCDs. Further along past the favorites things tend to get be grouped by genre after that by the scale above.
Ys games are on the Ys bookcase and Tengai Makyou games are on the Tengai Makyou bookcase.
I start the HuCards with System Card and Tennokoe Bank cases, then all CD style HuCard cases, then favoriteness until it averages out by matching spines.
Back in the day, I kept all double disc cases together. Which was tough, since racks that held them were hard to find.
Right now most of my Turbo/PCE games are on my two tall narrow Ikea CD rack towers.
The HuCard binders-
I need more binders and pages