I've got a drawer full of dozens of game manuals across many consoles, especially NES, SNES, Nintendo 64, GBA, and PC. While it's obvious that most manuals for modern games (in my case, Wii, GameCube, 3DS, DS, Xbox 360, Xbox, PS2, PlayStation, and some Sega Genesis) should be stored in their respective DVD/CD cases, I'm not sure what to do about the games that were sold in cardboard boxes (which were often thrown out). I lack most original cardboard boxes for games, and I typically take good care of my gaming products so I don't lose them.

My current best idea is to gather up a few plastic NES and N64 cases, typically used in video rental stores, and stack them neatly in there. I can easily put manuals with their respective games in the cases, such as Super Mario Bros. 3 or Rad Racer, but I actually have a lot of NES manuals for games that I don't own. Then there are the GBA games, which are far smaller than the manuals.

What do you folks think I should do with them?

Why would you keep manuals of games you no longer have?

Nostalgia purposes?

Anyway. I think your idea of plastic cartridges is a good one. I can't say much else, because I keep my old ones in a drawer as well.

You could try plastic, clamshell VHS cases. NES games may not fit but others like Genesis and N64 games will fit. Just avoid the ones with hubs/posts.