I like my Turbo games like I like my men. Black. +1 awesome points if you get that.
For hucards, I prefer getting loose, let the collectors have the cases and stuff. I do like manuals, but it's hardly a necessity since US manuals are largely useless, and the pretty Japanese manuals I can't read anyway. I put them in a large fake leather business card holder, organized by system cards and flash cart first, then by how much I like the game. It's kinda random, but it makes game selection easier on the go with the Turbo Express.
CD games, on the other hand, I get with case and manual in preferably mint condition. I don't care for the boxes or spine cards, however. I put them in a storage box in simple alphabetic order. It's not difficult, I only have a few CD games.