I do something similar to what you have. I've got a different tote box for every console, that contains the system if it isn't hooked up and all the connectors. This also works when I've got a box like my SNES box. I've got an original SNES and a slim, those are both in the box with almost all my controllers, hookups, and peripherals. Then connected to the TV is just the RetroDuo and the two controllers.
Then if I only have a few games for the system (CD-i, 3DO, TurboGrafx) I put those in the same box. Otherwise, I get those flatter tote boxes just for the games. I got clear boxes so I could easily see what was inside, and I bought a bunch all at once so they all match and stack well. I probably have close to 30 of these boxes.
Makes it really easy when I get in the mood for something specific..."Hmm, I want to play ColecoVision!" One box, two max, and I'm connected and enjoying. It's not ideal as I'd love to someday have everything connected, but for a person living in a townhouse this works very well.