Well, my Gamecube games are intermixed with my Wii games, and my GB, GBC, GBA, and DS games are intermixed, but they're separate from each other. When I buy the UGC, my cartridges will be separate from the disk based and the portable games. I haven't yet decided if I should intermix my Xbox 360 games and my PC games with my GCN and Wii games, but since I only have a couple of games for either (I'm fairly new to the world of Microsoft consoles, and most of my games for both Xbox 360 and PC are from the XBLA and Steam respectively), I'm not rushing to make that decision. I may, at a later date, decide to separate every game first by console, then UPC number, but for now I'm happy with how it's set up.
I'd add a picture to show you, but I don't have a working camera and I don't want to drive this thread anymore off topic.