Organize?
Hmm... That may be giving it too much credit. I guess I use the Goonies Method for cartridges. I dedicated an old dresser to it. The Atari 2600 goes in the top drawer. The Genesis and Nintendo go in the second drawer. And the Coleco/N64/others go in the bottom drawer. Always separate the drugs.... err games.
The only console cartridges not in there are the Odyessey 2 cartridges and they are in the same 8-track cases they have been in since the 70s.
Portable systems are in their own carrying cases and the games are in the cases as well.
Disc based systems? Sigh... those are just in Rubbermaid containers. I can't get too excited about doing anything with them. The 360 discs are still in the old DVD cases in the living room. I don't buy discs for the Xbox One or the PS4, much prefer digital for these systems so the one or two that we have are just tucked in with the 360 games.
The SNES/Super Famicom are an enigma. My wife is collecting those, currently they are in a collection of boxes, a couple for cleaned cartridges and a box or two for yet to be cleaned. What I do know is that once she decides what she wants to do with them, they will be indexed and alphabetized...