I like PC Engine style cases with manual and HuCard. I also like uniformity. So for pre-TTi releases that I didn't have cases for, I put Sparky labels on spare cases. Mostly damaged or super common/cheap game cases. For the rest which never came with cases, I use Aaron's 3D printed cases with Sparky labels. For missing manuals, I print out the front/back cover and fold it in half. To keep things consistent and games clean and to not worry about keeping track of original sleeves, I'm only using Seymor's new sleeves.
I have a couple CD games without original tray liner/inserts. But I feel the same about having PC Engine style games on cases, so I'm not realky concerned about cardboard boxes. I have several boxes, mostly from sealed games I've opened, but do not have plans to collect 'em all.
I'm planning on organizing my Turbo games and keeping TurboChips in cases soon. For the past 30'ish years though, I've kept HuCards loose in stacks for the most part. I couldn't tell you at any given time where Magical Chase is, only that it's definitely slevveless on a stack somewhere.